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
51,DRR029943,DRX026961,DRS086501,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,oocyte maturation duirng natural paring,zebrafish ovary isolated from adult fish at oocyte maturation duirng natural paring. [RNAseq],SAMD00025433,,sample name:5 OM|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025433,DRX026961,5 OM,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025433,,,,573617016.0,15933806.0,DRR029943,0:36,A:130606804;C:141376330;G:145891720;T:155734276;N:7886,36,,,,130606804,141376330,145891720,155734276,7886,DRX026961,DRS086501,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91108,,0.0173,,0.76205,,0.46319,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Multi-tissue,Multi-system
168,DRR075402,DRX069316,DRS075497,DRP004473,PRJDB5226,Effects of local gut tumor on whole organismal gene expressions in zebrafish,DRP004473,Other,How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.,,,The liver of tumor fish 7dpf,Tumor liver,SAMD00065416,,sample name:6 Tumor liver 150701 Hiseq3A l3 022|tissue type:Liver,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00065416,DRX069316,Tumor liver,1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004473,Illumina HiSeq 2500 sequencing of SAMD00065416,,,,1091167236.0,30310201.0,DRR075402,0:36,A:272216839;C:257523620;G:259746158;T:301642763;N:37856,36,,,,272216839,257523620,259746158,301642763,37856,DRX069316,DRS075497,DRA005199,"ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International","The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International",1,0.90443,,0.08935,,0.71863,,0.51145,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2018-09-19,Larval,Larval,Multi-tissue,Multi-system
169,DRR075401,DRX069315,DRS075496,DRP004473,PRJDB5226,Effects of local gut tumor on whole organismal gene expressions in zebrafish,DRP004473,Other,How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.,,,The gut of tumor fish 7dpf,Tumor gut,SAMD00065415,,sample name:5 Tumor gut 150701 Hiseq3A l3 021|tissue type:Gut,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00065415,DRX069315,Tumor gut,1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004473,Illumina HiSeq 2500 sequencing of SAMD00065415,,,,1423792872.0,39549802.0,DRR075401,0:36,A:342328685;C:346616167;G:341519547;T:393278536;N:49937,36,,,,342328685,346616167,341519547,393278536,49937,DRX069315,DRS075496,DRA005199,"ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International","The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International",1,0.91303,,0.0869,,0.70494,,0.44332,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2018-09-19,Larval,Larval,Multi-tissue,Multi-system
170,DRR075400,DRX069314,DRS075495,DRP004473,PRJDB5226,Effects of local gut tumor on whole organismal gene expressions in zebrafish,DRP004473,Other,How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.,,,The remaining part of body of tumor fish 7dpf,Tumor body,SAMD00065414,,sample name:4 Tumor body 150701 Hiseq3A l3 020|tissue type:Body,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00065414,DRX069314,Tumor body,1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004473,Illumina HiSeq 2500 sequencing of SAMD00065414,,,,1168514964.0,32458749.0,DRR075400,0:36,A:286579925;C:275496498;G:278133055;T:328265078;N:40408,36,,,,286579925,275496498,278133055,328265078,40408,DRX069314,DRS075495,DRA005199,"ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International","The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International",1,0.89927,,0.15051,,0.66714,,0.47579,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2018-09-19,Larval,Larval,Multi-tissue,Multi-system
175,DRR084197,DRX078028,DRS086522,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring early sample,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate2],SAMD00073604,,sample name:M 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073604,DRX078028,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073604,,,,1389837888.0,38606608.0,DRR084197,0:36,A:320671418;C:336948866;G:347550258;T:381720581;N:2946765,36,,,,320671418,336948866,347550258,381720581,2946765,DRX078028,DRS086522,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.89763,,0.02235,,0.76445,,0.46381,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Zygote,Embryo,Multi-tissue,Multi-system
181,DRR084191,DRX078022,DRS086516,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring early sample,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate1],SAMD00073598,,sample name:M|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073598,DRX078022,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073598,,,,1050981012.0,29193917.0,DRR084191,0:36,A:241048832;C:256186268;G:260277071;T:293299597;N:169244,36,,,,241048832,256186268,260277071,293299597,169244,DRX078022,DRS086516,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.9088,,0.02369,,0.7624,,0.47998,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Zygote,Embryo,Multi-tissue,Multi-system
36147,SRR33446914,SRX28687233,SRS24954089,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / uncut tail replicate 4,GSM8970925,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / uncut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated,GSM8970925,GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq,GSM8970925 r1,GSM8970925,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,White-4_S18_L001_R1_001.fastq.gz,fastq,392062720.0,5158720.0,GSM8970925 r1,0:76,A:111393933;C:84178440;G:86759120;T:109728583;N:2644,76,,,,111393933,84178440,86759120,109728583,2644,SRX28687233,SRS24954089,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36148,SRR33446915,SRX28687233,SRS24954089,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / uncut tail replicate 4,GSM8970925,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / uncut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated,GSM8970925,GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq,GSM8970925 r1,GSM8970925,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,White-4_S18_L002_R1_001.fastq.gz,fastq,382539160.0,5033410.0,GSM8970925 r2,0:76,A:108549273;C:82135694;G:84877971;T:106974218;N:2004,76,,,,108549273,82135694,84877971,106974218,2004,SRX28687233,SRS24954089,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36149,SRR33446916,SRX28687233,SRS24954089,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / uncut tail replicate 4,GSM8970925,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / uncut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated,GSM8970925,GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq,GSM8970925 r1,GSM8970925,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,White-4_S18_L003_R1_001.fastq.gz,fastq,390689020.0,5140645.0,GSM8970925 r3,0:76,A:110921885;C:83926202;G:86538209;T:109300187;N:2537,76,,,,110921885,83926202,86538209,109300187,2537,SRX28687233,SRS24954089,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36150,SRR33446917,SRX28687233,SRS24954089,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / uncut tail replicate 4,GSM8970925,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / uncut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated,GSM8970925,GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq,GSM8970925 r1,GSM8970925,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,White-4_S18_L004_R1_001.fastq.gz,fastq,385026032.0,5066132.0,GSM8970925 r4,0:76,A:109282089;C:82666299;G:85291625;T:107783812;N:2207,76,,,,109282089,82666299,85291625,107783812,2207,SRX28687233,SRS24954089,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36151,SRR33446918,SRX28687232,SRS24954088,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / uncut tail replicate 3,GSM8970924,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / uncut tail replicate 3,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated,GSM8970924,GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq,GSM8970924 r1,GSM8970924,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,White-3_S17_L001_R1_001.fastq.gz,fastq,242078544.0,3185244.0,GSM8970924 r1,0:76,A:70805011;C:50935537;G:52720022;T:67616569;N:1405,76,,,,70805011,50935537,52720022,67616569,1405,SRX28687232,SRS24954088,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36152,SRR33446919,SRX28687232,SRS24954088,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / uncut tail replicate 3,GSM8970924,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / uncut tail replicate 3,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated,GSM8970924,GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq,GSM8970924 r1,GSM8970924,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,White-3_S17_L002_R1_001.fastq.gz,fastq,236879840.0,3116840.0,GSM8970924 r2,0:76,A:69118193;C:49900432;G:51722708;T:66137243;N:1264,76,,,,69118193,49900432,51722708,66137243,1264,SRX28687232,SRS24954088,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36153,SRR33446920,SRX28687232,SRS24954088,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / uncut tail replicate 3,GSM8970924,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / uncut tail replicate 3,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated,GSM8970924,GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq,GSM8970924 r1,GSM8970924,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,White-3_S17_L003_R1_001.fastq.gz,fastq,241246952.0,3174302.0,GSM8970924 r3,0:76,A:70493049;C:50814403;G:52594412;T:67343618;N:1470,76,,,,70493049,50814403,52594412,67343618,1470,SRX28687232,SRS24954088,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36154,SRR33446921,SRX28687232,SRS24954088,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / uncut tail replicate 3,GSM8970924,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / uncut tail replicate 3,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated,GSM8970924,GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq,GSM8970924 r1,GSM8970924,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,White-3_S17_L004_R1_001.fastq.gz,fastq,238296936.0,3135486.0,GSM8970924 r4,0:76,A:69600911;C:50177666;G:51934697;T:66582348;N:1314,76,,,,69600911,50177666,51934697,66582348,1314,SRX28687232,SRS24954088,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36155,SRR33446922,SRX28687231,SRS24954087,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / uncut tail replicate 2,GSM8970923,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / uncut tail replicate 2,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated,GSM8970923,GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq,GSM8970923 r1,GSM8970923,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,White-2_S16_L001_R1_001.fastq.gz,fastq,293546884.0,3862459.0,GSM8970923 r1,0:76,A:86721485;C:61000183;G:63592308;T:82231012;N:1896,76,,,,86721485,61000183,63592308,82231012,1896,SRX28687231,SRS24954087,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36156,SRR33446923,SRX28687231,SRS24954087,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / uncut tail replicate 2,GSM8970923,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / uncut tail replicate 2,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated,GSM8970923,GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq,GSM8970923 r1,GSM8970923,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,White-2_S16_L002_R1_001.fastq.gz,fastq,287313668.0,3780443.0,GSM8970923 r2,0:76,A:84719789;C:59732524;G:62422596;T:80437282;N:1477,76,,,,84719789,59732524,62422596,80437282,1477,SRX28687231,SRS24954087,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36157,SRR33446924,SRX28687231,SRS24954087,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / uncut tail replicate 2,GSM8970923,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / uncut tail replicate 2,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated,GSM8970923,GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq,GSM8970923 r1,GSM8970923,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,White-2_S16_L003_R1_001.fastq.gz,fastq,293081612.0,3856337.0,GSM8970923 r3,0:76,A:86491724;C:60944765;G:63551581;T:82091805;N:1737,76,,,,86491724,60944765,63551581,82091805,1737,SRX28687231,SRS24954087,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36158,SRR33446925,SRX28687231,SRS24954087,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / uncut tail replicate 2,GSM8970923,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / uncut tail replicate 2,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated,GSM8970923,GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq,GSM8970923 r1,GSM8970923,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,White-2_S16_L004_R1_001.fastq.gz,fastq,289340284.0,3807109.0,GSM8970923 r4,0:76,A:85390241;C:60135471;G:62741618;T:81071340;N:1614,76,,,,85390241,60135471,62741618,81071340,1614,SRX28687231,SRS24954087,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36159,SRR33446926,SRX28687230,SRS24954086,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / cut tail replicate 4,GSM8970922,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / cut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated,GSM8970922,GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq,GSM8970922 r1,GSM8970922,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Red-4_S15_L001_R1_001.fastq.gz,fastq,293676616.0,3864166.0,GSM8970922 r1,0:76,A:85055525;C:61514402;G:62951777;T:84153135;N:1777,76,,,,85055525,61514402,62951777,84153135,1777,SRX28687230,SRS24954086,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36160,SRR33446927,SRX28687230,SRS24954086,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / cut tail replicate 4,GSM8970922,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / cut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated,GSM8970922,GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq,GSM8970922 r1,GSM8970922,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Red-4_S15_L002_R1_001.fastq.gz,fastq,287550712.0,3783562.0,GSM8970922 r2,0:76,A:83130155;C:60249305;G:61817163;T:82352632;N:1457,76,,,,83130155,60249305,61817163,82352632,1457,SRX28687230,SRS24954086,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36161,SRR33446928,SRX28687230,SRS24954086,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / cut tail replicate 4,GSM8970922,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / cut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated,GSM8970922,GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq,GSM8970922 r1,GSM8970922,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Red-4_S15_L003_R1_001.fastq.gz,fastq,293005460.0,3855335.0,GSM8970922 r3,0:76,A:84798214;C:61435286;G:62865004;T:83905146;N:1810,76,,,,84798214,61435286,62865004,83905146,1810,SRX28687230,SRS24954086,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36162,SRR33446929,SRX28687230,SRS24954086,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / cut tail replicate 4,GSM8970922,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / cut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated,GSM8970922,GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq,GSM8970922 r1,GSM8970922,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Red-4_S15_L004_R1_001.fastq.gz,fastq,289004668.0,3802693.0,GSM8970922 r4,0:76,A:83595831;C:60570265;G:62006632;T:82830364;N:1576,76,,,,83595831,60570265,62006632,82830364,1576,SRX28687230,SRS24954086,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36163,SRR33446930,SRX28687229,SRS24954085,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / cut tail replicate 3,GSM8970921,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / cut tail replicate 3,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated,GSM8970921,GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq,GSM8970921 r1,GSM8970921,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Red-3_S14_L001_R1_001.fastq.gz,fastq,300231768.0,3950418.0,GSM8970921 r1,0:76,A:88106516;C:61818857;G:65466450;T:84838096;N:1849,76,,,,88106516,61818857,65466450,84838096,1849,SRX28687229,SRS24954085,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36164,SRR33446931,SRX28687229,SRS24954085,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / cut tail replicate 3,GSM8970921,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / cut tail replicate 3,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated,GSM8970921,GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq,GSM8970921 r1,GSM8970921,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Red-3_S14_L002_R1_001.fastq.gz,fastq,293677452.0,3864177.0,GSM8970921 r2,0:76,A:86015379;C:60508410;G:64229226;T:82922956;N:1481,76,,,,86015379,60508410,64229226,82922956,1481,SRX28687229,SRS24954085,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36165,SRR33446932,SRX28687229,SRS24954085,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / cut tail replicate 3,GSM8970921,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / cut tail replicate 3,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated,GSM8970921,GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq,GSM8970921 r1,GSM8970921,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Red-3_S14_L003_R1_001.fastq.gz,fastq,299518280.0,3941030.0,GSM8970921 r3,0:76,A:87800455;C:61713738;G:65389216;T:84612972;N:1899,76,,,,87800455,61713738,65389216,84612972,1899,SRX28687229,SRS24954085,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36166,SRR33446933,SRX28687229,SRS24954085,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / cut tail replicate 3,GSM8970921,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / cut tail replicate 3,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated,GSM8970921,GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq,GSM8970921 r1,GSM8970921,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Red-3_S14_L004_R1_001.fastq.gz,fastq,295680204.0,3890529.0,GSM8970921 r4,0:76,A:86636984;C:60930934;G:64539123;T:83571354;N:1809,76,,,,86636984,60930934,64539123,83571354,1809,SRX28687229,SRS24954085,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36167,SRR33446934,SRX28687228,SRS24954084,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / cut tail replicate 2,GSM8970920,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / cut tail replicate 2,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated,GSM8970920,GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq,GSM8970920 r1,GSM8970920,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Red-2_S13_L001_R1_001.fastq.gz,fastq,266233396.0,3503071.0,GSM8970920 r1,0:76,A:78387833;C:55246603;G:58347116;T:74250158;N:1686,76,,,,78387833,55246603,58347116,74250158,1686,SRX28687228,SRS24954084,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36168,SRR33446935,SRX28687228,SRS24954084,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / cut tail replicate 2,GSM8970920,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / cut tail replicate 2,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated,GSM8970920,GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq,GSM8970920 r1,GSM8970920,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Red-2_S13_L002_R1_001.fastq.gz,fastq,260317404.0,3425229.0,GSM8970920 r2,0:76,A:76487964;C:54052872;G:57202492;T:72572684;N:1392,76,,,,76487964,54052872,57202492,72572684,1392,SRX28687228,SRS24954084,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36169,SRR33446936,SRX28687228,SRS24954084,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / cut tail replicate 2,GSM8970920,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / cut tail replicate 2,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated,GSM8970920,GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq,GSM8970920 r1,GSM8970920,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Red-2_S13_L003_R1_001.fastq.gz,fastq,265513676.0,3493601.0,GSM8970920 r3,0:76,A:78116084;C:55123773;G:58227738;T:74044386;N:1695,76,,,,78116084,55123773,58227738,74044386,1695,SRX28687228,SRS24954084,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36170,SRR33446937,SRX28687228,SRS24954084,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,SB 431542 treated / cut tail replicate 2,GSM8970920,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing,SB 431542 treated / cut tail replicate 2,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated,GSM8970920,GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq,GSM8970920 r1,GSM8970920,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Red-2_S13_L004_R1_001.fastq.gz,fastq,262010532.0,3447507.0,GSM8970920 r4,0:76,A:77058783;C:54402656;G:57452833;T:73094822;N:1438,76,,,,77058783,54402656,57452833,73094822,1438,SRX28687228,SRS24954084,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36171,SRR33446938,SRX28687227,SRS24954083,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / uncut tail replicate 4,GSM8970919,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing,DMSO treated / uncut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured,GSM8970919,GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq,GSM8970919 r1,GSM8970919,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Pink-4_S24_L001_R1_001.fastq.gz,fastq,334535736.0,4401786.0,GSM8970919 r1,0:76,A:104303278;C:67025244;G:65441286;T:97763807;N:2121,76,,,,104303278,67025244,65441286,97763807,2121,SRX28687227,SRS24954083,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36172,SRR33446939,SRX28687227,SRS24954083,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / uncut tail replicate 4,GSM8970919,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing,DMSO treated / uncut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured,GSM8970919,GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq,GSM8970919 r1,GSM8970919,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Pink-4_S24_L002_R1_001.fastq.gz,fastq,325405780.0,4281655.0,GSM8970919 r2,0:76,A:101185453;C:65289632;G:63869692;T:95059316;N:1687,76,,,,101185453,65289632,63869692,95059316,1687,SRX28687227,SRS24954083,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36173,SRR33446940,SRX28687227,SRS24954083,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / uncut tail replicate 4,GSM8970919,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing,DMSO treated / uncut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured,GSM8970919,GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq,GSM8970919 r1,GSM8970919,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Pink-4_S24_L003_R1_001.fastq.gz,fastq,333272540.0,4385165.0,GSM8970919 r3,0:76,A:103781471;C:66831319;G:65274288;T:97383334;N:2128,76,,,,103781471,66831319,65274288,97383334,2128,SRX28687227,SRS24954083,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36174,SRR33446941,SRX28687227,SRS24954083,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / uncut tail replicate 4,GSM8970919,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing,DMSO treated / uncut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured,GSM8970919,GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq,GSM8970919 r1,GSM8970919,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Pink-4_S24_L004_R1_001.fastq.gz,fastq,328778432.0,4326032.0,GSM8970919 r4,0:76,A:102340372;C:65917125;G:64384673;T:96134375;N:1887,76,,,,102340372,65917125,64384673,96134375,1887,SRX28687227,SRS24954083,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36175,SRR33446942,SRX28687226,SRS24954082,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / uncut tail replicate 2,GSM8970918,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing,DMSO treated / uncut tail replicate 2,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured,GSM8970918,GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq,GSM8970918 r1,GSM8970918,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Pink-2_S23_L001_R1_001.fastq.gz,fastq,254273428.0,3345703.0,GSM8970918 r1,0:76,A:73868437;C:53712396;G:55649268;T:71041836;N:1491,76,,,,73868437,53712396,55649268,71041836,1491,SRX28687226,SRS24954082,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36176,SRR33446943,SRX28687226,SRS24954082,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / uncut tail replicate 2,GSM8970918,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing,DMSO treated / uncut tail replicate 2,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured,GSM8970918,GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq,GSM8970918 r1,GSM8970918,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Pink-2_S23_L002_R1_001.fastq.gz,fastq,247479256.0,3256306.0,GSM8970918 r2,0:76,A:71749772;C:52269437;G:54304263;T:69154447;N:1337,76,,,,71749772,52269437,54304263,69154447,1337,SRX28687226,SRS24954082,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36177,SRR33446944,SRX28687226,SRS24954082,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / uncut tail replicate 2,GSM8970918,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing,DMSO treated / uncut tail replicate 2,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured,GSM8970918,GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq,GSM8970918 r1,GSM8970918,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Pink-2_S23_L003_R1_001.fastq.gz,fastq,252975424.0,3328624.0,GSM8970918 r3,0:76,A:73431938;C:53451559;G:55422676;T:70667726;N:1525,76,,,,73431938,53451559,55422676,70667726,1525,SRX28687226,SRS24954082,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36178,SRR33446945,SRX28687226,SRS24954082,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / uncut tail replicate 2,GSM8970918,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing,DMSO treated / uncut tail replicate 2,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured,GSM8970918,GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq,GSM8970918 r1,GSM8970918,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Pink-2_S23_L004_R1_001.fastq.gz,fastq,249310400.0,3280400.0,GSM8970918 r4,0:76,A:72326303;C:52679056;G:54605938;T:69697722;N:1381,76,,,,72326303,52679056,54605938,69697722,1381,SRX28687226,SRS24954082,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36179,SRR33446946,SRX28687225,SRS24954081,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / uncut tail replicate 1,GSM8970917,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing,DMSO treated / uncut tail replicate 1,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured,GSM8970917,GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq,GSM8970917 r1,GSM8970917,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Pink-1_S22_L001_R1_001.fastq.gz,fastq,270570108.0,3560133.0,GSM8970917 r1,0:76,A:78499185;C:56484520;G:59318322;T:76266342;N:1739,76,,,,78499185,56484520,59318322,76266342,1739,SRX28687225,SRS24954081,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36180,SRR33446947,SRX28687225,SRS24954081,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / uncut tail replicate 1,GSM8970917,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing,DMSO treated / uncut tail replicate 1,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured,GSM8970917,GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq,GSM8970917 r1,GSM8970917,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Pink-1_S22_L002_R1_001.fastq.gz,fastq,263995348.0,3473623.0,GSM8970917 r2,0:76,A:76492301;C:55131794;G:58036716;T:74333178;N:1359,76,,,,76492301,55131794,58036716,74333178,1359,SRX28687225,SRS24954081,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36181,SRR33446948,SRX28687225,SRS24954081,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / uncut tail replicate 1,GSM8970917,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing,DMSO treated / uncut tail replicate 1,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured,GSM8970917,GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq,GSM8970917 r1,GSM8970917,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Pink-1_S22_L003_R1_001.fastq.gz,fastq,269322036.0,3543711.0,GSM8970917 r3,0:76,A:78091756;C:56257589;G:59094882;T:75876132;N:1677,76,,,,78091756,56257589,59094882,75876132,1677,SRX28687225,SRS24954081,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36182,SRR33446949,SRX28687225,SRS24954081,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / uncut tail replicate 1,GSM8970917,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing,DMSO treated / uncut tail replicate 1,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Uninjured,GSM8970917,GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq,GSM8970917 r1,GSM8970917,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Pink-1_S22_L004_R1_001.fastq.gz,fastq,265691820.0,3495945.0,GSM8970917 r4,0:76,A:77002713;C:55467944;G:58293660;T:74926013;N:1490,76,,,,77002713,55467944,58293660,74926013,1490,SRX28687225,SRS24954081,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36183,SRR33446950,SRX28687224,SRS24954080,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / cut tail replicate 4,GSM8970916,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing,DMSO treated / cut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision,GSM8970916,GSM8970916: DMSO treated / cut tail replicate 4; Danio rerio; RNA Seq,GSM8970916 r1,GSM8970916,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Orange-4_S21_L001_R1_001.fastq.gz,fastq,349029392.0,4592492.0,GSM8970916 r1,0:76,A:99839652;C:73943935;G:76249851;T:98993782;N:2172,76,,,,99839652,73943935,76249851,98993782,2172,SRX28687224,SRS24954080,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36184,SRR33446951,SRX28687224,SRS24954080,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / cut tail replicate 4,GSM8970916,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing,DMSO treated / cut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision,GSM8970916,GSM8970916: DMSO treated / cut tail replicate 4; Danio rerio; RNA Seq,GSM8970916 r1,GSM8970916,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Orange-4_S21_L002_R1_001.fastq.gz,fastq,340876568.0,4485218.0,GSM8970916 r2,0:76,A:97335332;C:72249777;G:74668638;T:96621097;N:1724,76,,,,97335332,72249777,74668638,96621097,1724,SRX28687224,SRS24954080,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36185,SRR33446952,SRX28687224,SRS24954080,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / cut tail replicate 4,GSM8970916,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing,DMSO treated / cut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision,GSM8970916,GSM8970916: DMSO treated / cut tail replicate 4; Danio rerio; RNA Seq,GSM8970916 r1,GSM8970916,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Orange-4_S21_L003_R1_001.fastq.gz,fastq,347633196.0,4574121.0,GSM8970916 r3,0:76,A:99370315;C:73701054;G:75983700;T:98575995;N:2132,76,,,,99370315,73701054,75983700,98575995,2132,SRX28687224,SRS24954080,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36186,SRR33446953,SRX28687224,SRS24954080,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / cut tail replicate 4,GSM8970916,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing,DMSO treated / cut tail replicate 4,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision,GSM8970916,GSM8970916: DMSO treated / cut tail replicate 4; Danio rerio; RNA Seq,GSM8970916 r1,GSM8970916,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Orange-4_S21_L004_R1_001.fastq.gz,fastq,343592352.0,4520952.0,GSM8970916 r4,0:76,A:98157486;C:72839122;G:75134528;T:97459296;N:1920,76,,,,98157486,72839122,75134528,97459296,1920,SRX28687224,SRS24954080,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36187,SRR33446954,SRX28687223,SRS24954079,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / cut tail replicate 3,GSM8970915,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing,DMSO treated / cut tail replicate 3,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision,GSM8970915,GSM8970915: DMSO treated / cut tail replicate 3; Danio rerio; RNA Seq,GSM8970915 r1,GSM8970915,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Orange-3_S20_L001_R1_001.fastq.gz,fastq,304693500.0,4009125.0,GSM8970915 r1,0:76,A:89126862;C:63666599;G:66255160;T:85642963;N:1916,76,,,,89126862,63666599,66255160,85642963,1916,SRX28687223,SRS24954079,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36188,SRR33446955,SRX28687223,SRS24954079,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / cut tail replicate 3,GSM8970915,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing,DMSO treated / cut tail replicate 3,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision,GSM8970915,GSM8970915: DMSO treated / cut tail replicate 3; Danio rerio; RNA Seq,GSM8970915 r1,GSM8970915,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Orange-3_S20_L002_R1_001.fastq.gz,fastq,297396892.0,3913117.0,GSM8970915 r2,0:76,A:86844888;C:62174886;G:64844462;T:83531083;N:1573,76,,,,86844888,62174886,64844462,83531083,1573,SRX28687223,SRS24954079,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36189,SRR33446956,SRX28687223,SRS24954079,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / cut tail replicate 3,GSM8970915,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing,DMSO treated / cut tail replicate 3,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision,GSM8970915,GSM8970915: DMSO treated / cut tail replicate 3; Danio rerio; RNA Seq,GSM8970915 r1,GSM8970915,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Orange-3_S20_L003_R1_001.fastq.gz,fastq,303170840.0,3989090.0,GSM8970915 r3,0:76,A:88574880;C:63384769;G:65999210;T:85210123;N:1858,76,,,,88574880,63384769,65999210,85210123,1858,SRX28687223,SRS24954079,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36190,SRR33446957,SRX28687223,SRS24954079,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / cut tail replicate 3,GSM8970915,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing,DMSO treated / cut tail replicate 3,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision,GSM8970915,GSM8970915: DMSO treated / cut tail replicate 3; Danio rerio; RNA Seq,GSM8970915 r1,GSM8970915,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Orange-3_S20_L004_R1_001.fastq.gz,fastq,299538876.0,3941301.0,GSM8970915 r4,0:76,A:87486058;C:62643433;G:65200414;T:84207227;N:1744,76,,,,87486058,62643433,65200414,84207227,1744,SRX28687223,SRS24954079,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36191,SRR33446958,SRX28687222,SRS24954078,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / cut tail replicate 1,GSM8970914,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing,DMSO treated / cut tail replicate 1,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision,GSM8970914,GSM8970914: DMSO treated / cut tail replicate 1; Danio rerio; RNA Seq,GSM8970914 r1,GSM8970914,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Orange-1_S19_L001_R1_001.fastq.gz,fastq,356071020.0,4685145.0,GSM8970914 r1,0:76,A:101990320;C:75361307;G:78194540;T:100522661;N:2192,76,,,,101990320,75361307,78194540,100522661,2192,SRX28687222,SRS24954078,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36192,SRR33446959,SRX28687222,SRS24954078,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / cut tail replicate 1,GSM8970914,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing,DMSO treated / cut tail replicate 1,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision,GSM8970914,GSM8970914: DMSO treated / cut tail replicate 1; Danio rerio; RNA Seq,GSM8970914 r1,GSM8970914,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Orange-1_S19_L002_R1_001.fastq.gz,fastq,349258684.0,4595509.0,GSM8970914 r2,0:76,A:99883376;C:73952042;G:76902800;T:98518682;N:1784,76,,,,99883376,73952042,76902800,98518682,1784,SRX28687222,SRS24954078,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36193,SRR33446960,SRX28687222,SRS24954078,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / cut tail replicate 1,GSM8970914,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing,DMSO treated / cut tail replicate 1,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision,GSM8970914,GSM8970914: DMSO treated / cut tail replicate 1; Danio rerio; RNA Seq,GSM8970914 r1,GSM8970914,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Orange-1_S19_L003_R1_001.fastq.gz,fastq,355553156.0,4678331.0,GSM8970914 r3,0:76,A:101770613;C:75287760;G:78157774;T:100334741;N:2268,76,,,,101770613,75287760,78157774,100334741,2268,SRX28687222,SRS24954078,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36194,SRR33446961,SRX28687222,SRS24954078,SRP583344,PRJNA1259437,Inhibition of TGF beta signalling during zebrafish larval tail regeneration.,GSE296469,Transcriptome Analysis,This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.,,,,DMSO treated / cut tail replicate 1,GSM8970914,,source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing,DMSO treated / cut tail replicate 1,demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file,Larval tail,SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference,tissue:Larval tail|genotype:Wild type|treatment:Tail excision,GSM8970914,GSM8970914: DMSO treated / cut tail replicate 1; Danio rerio; RNA Seq,GSM8970914 r1,GSM8970914,1,100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP583344,,,Orange-1_S19_L004_R1_001.fastq.gz,fastq,351537316.0,4625491.0,GSM8970914 r4,0:76,A:100573823;C:74441165;G:77263744;T:99256707;N:1877,76,,,,100573823,74441165,77263744,99256707,1877,SRX28687222,SRS24954078,SRA2124571,University of Sheffield,University of Sheffield,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,United Kingdom,2025-05-06,Larval,Larval,Tail,Multi-system
36271,SRR298568,SRX079846,SRS212652,SRP007331,PRJNA141525,Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.,GSE29418,Transcriptome Analysis,RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.,,pubmed:21743441,,ZiwiIPTes,GSM727525,,tissue:RNA obtained from immunoprecipitation with Ziwi antibody from zebrafish testis extract|strain:TL,ZiwiIPTes,three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.,RNA obtained from immunoprecipitation with Ziwi antibody from zebrafish testis extract,,Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen  3 or 6 testes  and Ziwi antibody in a total volume of 500 µl.  RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis  adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.,,strain:TL,GSM727525,GSM727525: ZiwiIPTes,GSM727525: ZiwiIPTes,GSM727525: ZiwiIPTes,1,,GEO Accession:GSM727525,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP007331,,read name barcode proc directive:ignore,ZiwiIPTes.fastq,fastq,976120596.0,27114461.0,GSM727525 1,0:36,,36,,,,,,,,,SRX079846,SRS212652,SRA039167,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.10415,,0.03658,,0.96173,,0.30033,,36,,B,,usable mapping rate,illumina,early_illumina,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2011-05-20,Undetermined,Undetermined,Multi-tissue,Multi-system
36276,SRR298563,SRX079841,SRS212647,SRP007331,PRJNA141525,Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.,GSE29418,Transcriptome Analysis,RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.,,pubmed:21743441,,TDRD1IPshort,GSM727520,,tissue:RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract|strain:TL,TDRD1IPshort,three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.,RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract,,Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen  3 or 6 testes  and Tdrd1 antibody 1:100 in a total volume of 500 µl.  RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis  adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.,,strain:TL,GSM727520,GSM727520: TDRD1IPshort,GSM727520: TDRD1IPshort,GSM727520: TDRD1IPshort,1,,GEO Accession:GSM727520,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP007331,,read name barcode proc directive:ignore,TDRD1IPshort.fastq,fastq,957724884.0,26603469.0,GSM727520 1,0:36,,36,,,,,,,,,SRX079841,SRS212647,SRA039167,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.10539,,0.05124,,0.93935,,0.34909,,36,,B,,usable mapping rate,illumina,early_illumina,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2011-05-20,Undetermined,Undetermined,Multi-tissue,Multi-system
36277,SRR298562,SRX079840,SRS212646,SRP007331,PRJNA141525,Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.,GSE29418,Transcriptome Analysis,RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.,,pubmed:21743441,,TDRD1IPlong,GSM727519,,tissue:RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract|strain:TL,TDRD1IPlong,three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.,RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract,,Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen  3 or 6 testes  and Tdrd1 antibody 1:100 in a total volume of 500 µl.  For cDNA synthesis  the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.,,strain:TL,GSM727519,GSM727519: TDRD1IPlong,GSM727519: TDRD1IPlong,GSM727519: TDRD1IPlong,1,,GEO Accession:GSM727519,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP007331,,read name barcode proc directive:ignore,TDRD1IPlong.fastq,fastq,1098157770.0,23872995.0,GSM727519 1,0:46,,46,,,,,,,,,SRX079840,SRS212646,SRA039167,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.63282,,0.29001,,0.80095,,0.51046,,46,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2011-05-20,Undetermined,Undetermined,Multi-tissue,Multi-system
36478,SRR527835,SRX171222,SRS352108,SRP014596,PRJNA171539,Transcriptomic analysis of zebrafish during development and homeostasis,GSE39703,Transcriptome Analysis,Sequencing libraries were generated from total RNA samples following the mRNAseq protocol for the generation of single end 16 hpf 36 hpf  5 day larvae  adult head and adult tail or paired end 24 hpf libraries Illumina. Single end reads of 36 nucleotides and paired end reads 2 x 76 nucleotides were obtained with a GAIIx Illumina. Gene expression at the different stages/tissu was assessed by cufflinks and HTseq. Overall design: RNAseq on 5 differents samples:  24hpf embryos  pool of 16 hour to 36 hour embryos  5 dpf larvea  adult head and adult tail,,pubmed:23684812,,tail,GSM977960,,tissue:entire adult tail|genotype:Wild type|strain:AB|Stage:adult tail,tail,Basecalls performed using CASAVA version 1.4 Reads aligned to zebrafish genome Zv9 Ensembl with Tophat v 1.4.1 and Bowtie v 0.12.7  options: butterfly search coverage search  microexon search  min anchor length 5   G GTF Determination of raw reads aligned to ZV9 with HTSeq v0.5.3p3 and gtf file ensembl zv9 release 60 Determination of RPKM/FPKM with cufflinks v 1.3.0 with the options  u  b  M rRNA/Mtgenes mask  G gtf Genome build: Zv9 v 60 Supplementary files format and content: *.count file are the output of Htseq reads quantification. *.fpkm files are the output of cufflinks quantification,entire adult tail,,Extraction of total RNA with Trizol following manufacturer's instruction. Generation of mRNA libraries with Trueseq RNA kit following Illumina's instructions,,genotype:Wild type|strain:AB|Stage:adult tail,GSM977960,GSM977960: tail; Danio rerio; RNA Seq,GSM977960 1,GSM977960: tail,1,,GEO Accession:GSM977960,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP014596,,,,,534897504.0,14858264.0,GSM977960 r1,0:36,A:144900139;C:122639505;G:130189210;T:136990883;N:177767,36,,,,144900139,122639505,130189210,136990883,177767,SRX171222,SRS352108,SRA056408,GEO,ITG,1,0.89933,,0.04578,,0.71254,,0.41668,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Unknown,2012-07-27,Adult,Adult,Tail,Multi-system
36560,SRR1048073,SRX363298,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish Brain miRNA,Brain miRNA,1,Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al.  2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles  and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light  and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle  corresponding to CT2  6  10  14  18 and 22. For miR seq  18 pineal glands were pooled from the 6 sampling times for both light and dark treatments  and one brain pool was composed of 4 brains that were collected from light  and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen.  miRNA capturing and library construction  for the pineal light  pineal dark and brain samples  were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly  three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx  then five prime adapter was added using T4 RNA Ligase with ATP. postwards  reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally  gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The three mature miRNA libraries pineal light  pineal dark  and brain were sequenced with bar codes on one lane of an Illumina HiSeq2000 instrument following the manufacturer’s protocol. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed. The total number of reads post filtering was 6 million  10.4 million and 14.8 million for the pineal light  pineal dark and brain  respectively.,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>,SRP016132,,,ZB_trimmed.fastq,fastq,323899236.0,14781569.0,Brain miRNA run,0:21.91 1:0,A:77705253;C:63882329;G:85902986;T:96383552;N:25116,21,0,,,77705253,63882329,85902986,96383552,25116,SRX363298,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,1,0.88754,,0.06569,,0.96747,,0.53358,,23,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Israel,2015-07-22,Adult,Adult,Multi-tissue,Multi-system
36561,SRR1048072,SRX363297,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland dark miRNA,Pineal gland dark miRNA,1,Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al.  2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles  and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light  and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle  corresponding to CT2  6  10  14  18 and 22. For miR seq  18 pineal glands were pooled from the 6 sampling times for both light and dark treatments  and one brain pool was composed of 4 brains that were collected from light  and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen.  miRNA capturing and library construction  for the pineal light  pineal dark and brain samples  were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly  three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx  then five prime adapter was added using T4 RNA Ligase with ATP. postwards  reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally  gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The three mature miRNA libraries pineal light  pineal dark  and brain were sequenced with bar codes on one lane of an Illumina HiSeq2000 instrument following the manufacturer’s protocol. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed. The total number of reads post filtering was 6 million  10.4 million and 14.8 million for the pineal light  pineal dark and brain  respectively.,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>,SRP016132,,,D_trimmed.fastq,fastq,231371620.0,10385264.0,Pineal gland dark miRNA run,0:22.28 1:0,A:61228408;C:44264639;G:58700027;T:67159878;N:18668,22,0,,,61228408,44264639,58700027,67159878,18668,SRX363297,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,1,0.84648,,0.04467,,0.95645,,0.79978,,22,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Israel,2015-07-22,Adult,Adult,Multi-tissue,Multi-system
36562,SRR1048071,SRX363296,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland light miRNA,Pineal gland light miRNA,1,Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al.  2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles  and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light  and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle  corresponding to CT2  6  10  14  18 and 22. For miR seq  18 pineal glands were pooled from the 6 sampling times for both light and dark treatments  and one brain pool was composed of 4 brains that were collected from light  and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen.  miRNA capturing and library construction  for the pineal light  pineal dark and brain samples  were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly  three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx  then five prime adapter was added using T4 RNA Ligase with ATP. postwards  reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally  gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The three mature miRNA libraries pineal light  pineal dark  and brain were sequenced with bar codes on one lane of an Illumina HiSeq2000 instrument following the manufacturer’s protocol. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed. The total number of reads post filtering was 6 million  10.4 million and 14.8 million for the pineal light  pineal dark and brain  respectively.,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>,SRP016132,,,L_trimmed.fastq,fastq,132417471.0,5933638.0,Pineal gland light miRNA run,0:22.32 1:0,A:36017069;C:26569684;G:32546616;T:37273526;N:10576,22,0,,,36017069,26569684,32546616,37273526,10576,SRX363296,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,1,0.86427,,0.03426,,0.95631,,0.86509,,21,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Israel,2015-07-22,Adult,Adult,Multi-tissue,Multi-system
36707,SRR835172,SRX271968,SRS416264,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,il 97h 42 440,GSM1129630,,tissue:iridophores|hpf,il 97h 42 440,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,iridophores,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129630,GSM1129630: il 97h 42 440; Danio rerio; RNA Seq,GSM1129630 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129630,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,il_97h_42_440.fq.bz2,fastq,113120952.0,2693356.0,GSM1129630 r1,0:42,A:26578283;C:27647612;G:26417805;T:32470133;N:7119,42,,,,26578283,27647612,26417805,32470133,7119,SRX271968,SRS416264,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",1,0.85151,,0.08761,,0.85766,,0.53122,,42,,B,,usable mapping rate,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Multi-tissue,Multi-system
36708,SRR835171,SRX271967,SRS416263,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,il 77h 49 440,GSM1129629,,tissue:iridophores|hpf,il 77h 49 440,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,iridophores,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129629,GSM1129629: il 77h 49 440; Danio rerio; RNA Seq,GSM1129629 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129629,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,il_77h_49_440.fq.bz2,fastq,119102886.0,2835783.0,GSM1129629 r1,0:42,A:27449590;C:27743213;G:26605006;T:37297547;N:7530,42,,,,27449590,27743213,26605006,37297547,7530,SRX271967,SRS416263,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",1,0.85274,,0.12109,,0.86239,,0.52589,,42,,B,,usable mapping rate,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Multi-tissue,Multi-system
36709,SRR835170,SRX271966,SRS416261,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,il 77h 44 440,GSM1129628,,tissue:iridophores|hpf,il 77h 44 440,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,iridophores,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129628,GSM1129628: il 77h 44 440; Danio rerio; RNA Seq,GSM1129628 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129628,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,il_77h_44_440.fq.bz2,fastq,319536210.0,7608005.0,GSM1129628 r1,0:42,A:72602262;C:81003831;G:76662728;T:89248984;N:18405,42,,,,72602262,81003831,76662728,89248984,18405,SRX271966,SRS416261,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",1,0.88506,,0.08161,,0.85756,,0.50585,,42,,B,,usable mapping rate,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Multi-tissue,Multi-system
36710,SRR835169,SRX271965,SRS416262,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,il 77h 38 351,GSM1129627,,tissue:iridophores|hpf,il 77h 38 351,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,iridophores,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129627,GSM1129627: il 77h 38 351; Danio rerio; RNA Seq,GSM1129627 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129627,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,il_77h_38_351_AGTGT.fq.bz2,fastq,105470208.0,2929728.0,GSM1129627 r1,0:36,A:23660397;C:24772356;G:27192539;T:29844080;N:836,36,,,,23660397,24772356,27192539,29844080,836,SRX271965,SRS416262,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",1,0.76356,,0.07685,,0.86634,,0.51592,,36,,B,,usable mapping rate,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Multi-tissue,Multi-system
36711,SRR835168,SRX271964,SRS416260,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,il 58h 50 440,GSM1129626,,tissue:iridophores|hpf,il 58h 50 440,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,iridophores,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129626,GSM1129626: il 58h 50 440; Danio rerio; RNA Seq,GSM1129626 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129626,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,il_58h_50_440.fq.bz2,fastq,158731692.0,3779326.0,GSM1129626 r1,0:42,A:35358330;C:37377423;G:36834086;T:49152866;N:8987,42,,,,35358330,37377423,36834086,49152866,8987,SRX271964,SRS416260,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",1,0.78748,,0.04211,,0.88183,,0.51498,,42,,B,,usable mapping rate,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Multi-tissue,Multi-system
38049,SRR1519899,SRX657112,SRS662299,SRP044634,PRJNA255636,mRNA sequencing of embryonic tails of sih mutants at 28 hpf,GSE59563,Transcriptome Analysis,We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf,,,,sih3,GSM1439473,,tissue:tail derived cells|genotype/variation:sih|embryonic stage:28 hpf,sih3,Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id  Gene name and one column for each sample containing the normalized read counts,tail derived cells,sih embryos lack heart contraction,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,Embryos were grown in normal conditions,genotype/variation:sih|embryonic stage:28 hpf,GSM1439473,GSM1439473: sih3; Danio rerio; RNA Seq,GSM1439473,,1,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,GEO Accession:GSM1439473,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP044634,,,JGZ-06.fastq.gz,fastq,1416036978.0,26222907.0,GSM1439473 r1,0:54,A:342287675;C:370618836;G:361870457;T:341179934;N:80076,54,,,,342287675,370618836,361870457,341179934,80076,SRX657112,SRS662299,SRA175990,GEO,IGBMC,1,0.96217,,0.03055,,0.76869,,0.44925,,54,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2014-07-18,Pharyngula,Embryo,Tail,Multi-system
38050,SRR1519898,SRX657111,SRS662291,SRP044634,PRJNA255636,mRNA sequencing of embryonic tails of sih mutants at 28 hpf,GSE59563,Transcriptome Analysis,We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf,,,,WT3,GSM1439472,,tissue:tail derived cells|genotype/variation:WT|embryonic stage:28 hpf,WT3,Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id  Gene name and one column for each sample containing the normalized read counts,tail derived cells,sih embryos lack heart contraction,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,Embryos were grown in normal conditions,genotype/variation:WT|embryonic stage:28 hpf,GSM1439472,GSM1439472: WT3; Danio rerio; RNA Seq,GSM1439472,,1,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,GEO Accession:GSM1439472,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP044634,,,JGZ-05.fastq.gz,fastq,1787680692.0,33105198.0,GSM1439472 r1,0:54,A:442553431;C:457003567;G:446438405;T:441598672;N:86617,54,,,,442553431,457003567,446438405,441598672,86617,SRX657111,SRS662291,SRA175990,GEO,IGBMC,1,0.96318,,0.03918,,0.75371,,0.4423,,54,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2014-07-18,Pharyngula,Embryo,Tail,Multi-system
38051,SRR1519897,SRX657110,SRS662290,SRP044634,PRJNA255636,mRNA sequencing of embryonic tails of sih mutants at 28 hpf,GSE59563,Transcriptome Analysis,We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf,,,,sih2,GSM1439471,,tissue:tail derived cells|genotype/variation:sih|embryonic stage:28 hpf,sih2,Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id  Gene name and one column for each sample containing the normalized read counts,tail derived cells,sih embryos lack heart contraction,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,Embryos were grown in normal conditions,genotype/variation:sih|embryonic stage:28 hpf,GSM1439471,GSM1439471: sih2; Danio rerio; RNA Seq,GSM1439471,,1,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,GEO Accession:GSM1439471,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP044634,,,JGZ-04.fastq.gz,fastq,1813069386.0,33575359.0,GSM1439471 r1,0:54,A:462594376;C:449896725;G:440482879;T:460019095;N:76311,54,,,,462594376,449896725,440482879,460019095,76311,SRX657110,SRS662290,SRA175990,GEO,IGBMC,1,0.95859,,0.05282,,0.74199,,0.47244,,54,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2014-07-18,Pharyngula,Embryo,Tail,Multi-system
38052,SRR1519896,SRX657109,SRS662289,SRP044634,PRJNA255636,mRNA sequencing of embryonic tails of sih mutants at 28 hpf,GSE59563,Transcriptome Analysis,We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf,,,,WT2,GSM1439470,,tissue:tail derived cells|genotype/variation:WT|embryonic stage:28 hpf,WT2,Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id  Gene name and one column for each sample containing the normalized read counts,tail derived cells,sih embryos lack heart contraction,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,Embryos were grown in normal conditions,genotype/variation:WT|embryonic stage:28 hpf,GSM1439470,GSM1439470: WT2; Danio rerio; RNA Seq,GSM1439470,,1,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,GEO Accession:GSM1439470,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP044634,,,JGZ-03.fastq.gz,fastq,1866194316.0,34559154.0,GSM1439470 r1,0:54,A:483946414;C:453986455;G:443561481;T:484623941;N:76025,54,,,,483946414,453986455,443561481,484623941,76025,SRX657109,SRS662289,SRA175990,GEO,IGBMC,1,0.95615,,0.06195,,0.73594,,0.47144,,54,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2014-07-18,Pharyngula,Embryo,Tail,Multi-system
38053,SRR1519895,SRX657108,SRS662288,SRP044634,PRJNA255636,mRNA sequencing of embryonic tails of sih mutants at 28 hpf,GSE59563,Transcriptome Analysis,We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf,,,,sih1,GSM1439469,,tissue:tail derived cells|genotype/variation:sih|embryonic stage:28 hpf,sih1,Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id  Gene name and one column for each sample containing the normalized read counts,tail derived cells,sih embryos lack heart contraction,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,Embryos were grown in normal conditions,genotype/variation:sih|embryonic stage:28 hpf,GSM1439469,GSM1439469: sih1; Danio rerio; RNA Seq,GSM1439469,,1,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,GEO Accession:GSM1439469,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP044634,,,JGZ-02.fastq.gz,fastq,1451212470.0,26874305.0,GSM1439469 r1,0:54,A:368354355;C:360129390;G:353350795;T:369317437;N:60493,54,,,,368354355,360129390,353350795,369317437,60493,SRX657108,SRS662288,SRA175990,GEO,IGBMC,1,0.94911,,0.04509,,0.74604,,0.46107,,54,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2014-07-18,Pharyngula,Embryo,Tail,Multi-system
38054,SRR1519894,SRX657107,SRS662287,SRP044634,PRJNA255636,mRNA sequencing of embryonic tails of sih mutants at 28 hpf,GSE59563,Transcriptome Analysis,We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf,,,,WT1,GSM1439468,,tissue:tail derived cells|genotype/variation:WT|embryonic stage:28 hpf,WT1,Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id  Gene name and one column for each sample containing the normalized read counts,tail derived cells,sih embryos lack heart contraction,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,Embryos were grown in normal conditions,genotype/variation:WT|embryonic stage:28 hpf,GSM1439468,GSM1439468: WT1; Danio rerio; RNA Seq,GSM1439468,,1,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,GEO Accession:GSM1439468,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP044634,,,JGZ-01.fastq.gz,fastq,1583485146.0,29323799.0,GSM1439468 r1,0:54,A:405051413;C:391145102;G:382645289;T:404569188;N:74154,54,,,,405051413,391145102,382645289,404569188,74154,SRX657107,SRS662287,SRA175990,GEO,IGBMC,1,0.94743,,0.05464,,0.73156,,0.46572,,54,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2014-07-18,Pharyngula,Embryo,Tail,Multi-system
40439,SRR3144620,SRX1560771,SRS1275344,SRP069287,PRJNA310829,Danio rerio strain:AB Raw sequence reads,PRJNA310829,Other,transcriptional profile of both macrophages M and endothelial end cells EC between three different lesion stages uninjured control con  upon macrophage arrival arr  and during macrophage traction tra.,,,,,macrophage and endothelial cells,,strain:AB|age:Day3|sex:not determined|tissue:macrophage and endothelial cells|BioSampleModel:Model organism or animal,,,,,,,,,Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction,macrophage and endothelial cells,1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>,SRP069287,,,EC-con-2-27_1.fq.gz,fastq,2627841170.0,26309124.0,macrophages and endothelial cells,0:99.88 1:0,A:787503280;C:537314192;G:533698336;T:769265722;N:59640,99,0,,,787503280,537314192,533698336,769265722,59640,SRX1560771,SRS1275344,SRA347117,SouthWest university Of China|Laboratory of Molecular Developmental Biology,Southwest University of China,1,0.87616,,0.42753,,0.88477,,0.63864,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2016-02-23,Larval,Larval,Multi-tissue,Multi-system
40947,SRR3465556,SRX1735458,SRS1416510,SRP074122,PRJNA319956,Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.,GSE80768,Transcriptome Analysis,Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.,,pubmed:27783941,,9267X14 tumor,GSM2136824,,source name:brain tumor|tissue:brain tumor,9267X14 tumor,USeq’s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq’s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq’s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values,brain tumor,Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.,tissue:brain tumor,GSM2136824,GSM2136824: 9267X14 tumor; Danio rerio; RNA Seq,GSM2136824,,1,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,GEO Accession:GSM2136824,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP074122,,,9267X14_120613_SN141_0510_AC0TF4ACXX_8.txt.gz,fastq,1403474100.0,28069482.0,GSM2136824 r1,0:50,A:379029580;C:327462448;G:316163138;T:380761095;N:57839,50,,,,379029580,327462448,316163138,380761095,57839,SRX1735458,SRS1416510,SRA421168,GEO,"Oncological Sciences, University of Utah",1,0.91779,,0.10471,,0.68018,,0.46831,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-28,Undetermined,Undetermined,Multi-tissue,Multi-system
40948,SRR3465555,SRX1735457,SRS1416511,SRP074122,PRJNA319956,Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.,GSE80768,Transcriptome Analysis,Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.,,pubmed:27783941,,9267X13 tumor,GSM2136823,,source name:brain tumor|tissue:brain tumor,9267X13 tumor,USeq’s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq’s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq’s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values,brain tumor,Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.,tissue:brain tumor,GSM2136823,GSM2136823: 9267X13 tumor; Danio rerio; RNA Seq,GSM2136823,,1,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,GEO Accession:GSM2136823,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP074122,,,9267X13_120613_SN141_0510_AC0TF4ACXX_8.txt.gz,fastq,1055273100.0,21105462.0,GSM2136823 r1,0:50,A:284702255;C:246805964;G:238397873;T:285323357;N:43651,50,,,,284702255,246805964,238397873,285323357,43651,SRX1735457,SRS1416511,SRA421168,GEO,"Oncological Sciences, University of Utah",1,0.92157,,0.09143,,0.73494,,0.47743,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-28,Undetermined,Undetermined,Multi-tissue,Multi-system
40949,SRR3465554,SRX1735456,SRS1416509,SRP074122,PRJNA319956,Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.,GSE80768,Transcriptome Analysis,Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.,,pubmed:27783941,,9267X12 tumor,GSM2136822,,source name:brain tumor|tissue:brain tumor,9267X12 tumor,USeq’s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq’s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq’s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values,brain tumor,Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.,tissue:brain tumor,GSM2136822,GSM2136822: 9267X12 tumor; Danio rerio; RNA Seq,GSM2136822,,1,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,GEO Accession:GSM2136822,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP074122,,,9267X12_120613_SN141_0510_AC0TF4ACXX_8.txt.gz,fastq,1235405300.0,24708106.0,GSM2136822 r1,0:50,A:334940379;C:286734309;G:278305987;T:335374199;N:50426,50,,,,334940379,286734309,278305987,335374199,50426,SRX1735456,SRS1416509,SRA421168,GEO,"Oncological Sciences, University of Utah",1,0.91587,,0.10088,,0.68107,,0.48664,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-28,Undetermined,Undetermined,Multi-tissue,Multi-system
40950,SRR3465553,SRX1735455,SRS1416508,SRP074122,PRJNA319956,Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.,GSE80768,Transcriptome Analysis,Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.,,pubmed:27783941,,9267X8 tumor,GSM2136821,,source name:brain tumor|tissue:brain tumor,9267X8 tumor,USeq’s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq’s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq’s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values,brain tumor,Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.,tissue:brain tumor,GSM2136821,GSM2136821: 9267X8 tumor; Danio rerio; RNA Seq,GSM2136821,,1,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,GEO Accession:GSM2136821,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP074122,,,9267X8_120613_SN141_0510_AC0TF4ACXX_7.txt.gz,fastq,1049619800.0,20992396.0,GSM2136821 r1,0:50,A:284508112;C:243447832;G:236471909;T:285153684;N:38263,50,,,,284508112,243447832,236471909,285153684,38263,SRX1735455,SRS1416508,SRA421168,GEO,"Oncological Sciences, University of Utah",1,0.92111,,0.10635,,0.68061,,0.48665,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-28,Undetermined,Undetermined,Multi-tissue,Multi-system
40951,SRR3465552,SRX1735454,SRS1416507,SRP074122,PRJNA319956,Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.,GSE80768,Transcriptome Analysis,Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.,,pubmed:27783941,,9267X7 tumor,GSM2136820,,source name:brain tumor|tissue:brain tumor,9267X7 tumor,USeq’s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq’s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq’s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values,brain tumor,Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.,tissue:brain tumor,GSM2136820,GSM2136820: 9267X7 tumor; Danio rerio; RNA Seq,GSM2136820,,1,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,GEO Accession:GSM2136820,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP074122,,,9267X7_120613_SN141_0510_AC0TF4ACXX_7.txt.gz,fastq,1050373350.0,21007467.0,GSM2136820 r1,0:50,A:283795799;C:244445968;G:237807604;T:284286043;N:37936,50,,,,283795799,244445968,237807604,284286043,37936,SRX1735454,SRS1416507,SRA421168,GEO,"Oncological Sciences, University of Utah",1,0.91684,,0.09541,,0.70808,,0.4782,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-28,Undetermined,Undetermined,Multi-tissue,Multi-system
40952,SRR3465551,SRX1735453,SRS1416506,SRP074122,PRJNA319956,Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.,GSE80768,Transcriptome Analysis,Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.,,pubmed:27783941,,9267X6 tumor,GSM2136819,,source name:brain tumor|tissue:brain tumor,9267X6 tumor,USeq’s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq’s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq’s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values,brain tumor,Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.,tissue:brain tumor,GSM2136819,GSM2136819: 9267X6 tumor; Danio rerio; RNA Seq,GSM2136819,,1,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,GEO Accession:GSM2136819,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP074122,,,9267X6_120613_SN141_0510_AC0TF4ACXX_7.txt.gz,fastq,909187300.0,18183746.0,GSM2136819 r1,0:50,A:246296969;C:211315305;G:203857359;T:247684298;N:33369,50,,,,246296969,211315305,203857359,247684298,33369,SRX1735453,SRS1416506,SRA421168,GEO,"Oncological Sciences, University of Utah",1,0.92029,,0.11221,,0.68578,,0.47422,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-28,Undetermined,Undetermined,Multi-tissue,Multi-system
40953,SRR3465550,SRX1735452,SRS1416505,SRP074122,PRJNA319956,Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.,GSE80768,Transcriptome Analysis,Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.,,pubmed:27783941,,9267X5 tumor,GSM2136818,,source name:brain tumor|tissue:brain tumor,9267X5 tumor,USeq’s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq’s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq’s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values,brain tumor,Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.,tissue:brain tumor,GSM2136818,GSM2136818: 9267X5 tumor; Danio rerio; RNA Seq,GSM2136818,,1,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,GEO Accession:GSM2136818,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP074122,,,9267X5_120613_SN141_0510_AC0TF4ACXX_7.txt.gz,fastq,1030064550.0,20601291.0,GSM2136818 r1,0:50,A:275570887;C:242993408;G:235025540;T:276437064;N:37651,50,,,,275570887,242993408,235025540,276437064,37651,SRX1735452,SRS1416505,SRA421168,GEO,"Oncological Sciences, University of Utah",1,0.91852,,0.0986,,0.70451,,0.47961,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-28,Undetermined,Undetermined,Multi-tissue,Multi-system
41035,SRR3581677,SRX1797273,SRS1465195,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Fluorescence activated cell sorted macrophages4,iRed4,,breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages from kidney|BioSampleModel:Model organism or animal,,,,,,,,,iRed4,iRed4,iRed4,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,iRed4.fastq.gz,fastq,2577391029.0,50537079.0,iRed4.fastq.gz,0:51,A:740368299;C:555561208;G:558570747;T:722870515;N:20260,51,,,,740368299,555561208,558570747,722870515,20260,SRX1797273,SRS1465195,SRA429040,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.87886,,0.09748,,0.75676,,0.49364,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2016-05-25,Adult,Adult,Multi-tissue,Multi-system
41036,SRR3581675,SRX1797272,SRS1465194,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Fluorescence activated cell sorted macrophages3,iRed3,,breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages from kidney|BioSampleModel:Model organism or animal,,,,,,,,,iRed3,iRed3,iRed3,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,iRed3.fastq.gz,fastq,2300094339.0,45099889.0,iRed3.fastq.gz,0:51,A:664396273;C:491535578;G:495836023;T:648307877;N:18588,51,,,,664396273,491535578,495836023,648307877,18588,SRX1797272,SRS1465194,SRA429039,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.88281,,0.15449,,0.75507,,0.47198,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Adult,Adult,Multi-tissue,Multi-system
41037,SRR3581674,SRX1797271,SRS1465193,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Fluorescence activated cell sorted macrophages2,iRed2,,breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages from kidney|BioSampleModel:Model organism or animal,,,,,,,,,iRed2,iRed2,iRed2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,iRed2.fastq.gz,fastq,1652550807.0,32402957.0,iRed2.fastq.gz,0:51,A:528348867;C:306088006;G:305625547;T:512475625;N:12762,51,,,,528348867,306088006,305625547,512475625,12762,SRX1797271,SRS1465193,SRA429038,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.83699,,0.16858,,0.76688,,0.49036,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2016-05-25,Adult,Adult,Multi-tissue,Multi-system
41312,SRR4199307,SRX2148087,SRS1679265,SRP087617,PRJNA342262,Proliferation independent regulation of organ size by Notch signaling,GSE86571,Transcriptome Analysis,Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow  we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails  with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate  using HiSeq 2500 Illumina.,,pubmed:28085667,,NICD rep3,GSM2306087,,source name:dissociated embryo tails|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf,NICD rep3,Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters  p 8   transcriptome index  G  o   no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters  p 4  g  o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters  m intersection nonempty  s no  f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample  one includes FPKM values for each Sample.,dissociated embryo tails,Zebrafish embryos positive for GFP were selected.,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.,strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf,GSM2306087,GSM2306087: NICD rep3; Danio rerio; RNA Seq,GSM2306087,,1,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2306087,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP087617,,,mutant3.fastq.gz,fastq,1706861931.0,33467881.0,GSM2306087 r1,0:51 1:0,A:400027681;C:444926525;G:399939257;T:461913972;N:54496,51,0,,,400027681,444926525,399939257,461913972,54496,SRX2148087,SRS1679265,SRA464955,GEO,Stowers Institute for Medical Research,1,0.75848,,0.06958,,0.73616,,0.47901,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2016-09-08,Pharyngula,Embryo,Tail,Multi-system
41313,SRR4199306,SRX2148086,SRS1679264,SRP087617,PRJNA342262,Proliferation independent regulation of organ size by Notch signaling,GSE86571,Transcriptome Analysis,Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow  we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails  with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate  using HiSeq 2500 Illumina.,,pubmed:28085667,,NICD rep2,GSM2306086,,source name:dissociated embryo tails|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf,NICD rep2,Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters  p 8   transcriptome index  G  o   no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters  p 4  g  o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters  m intersection nonempty  s no  f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample  one includes FPKM values for each Sample.,dissociated embryo tails,Zebrafish embryos positive for GFP were selected.,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.,strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf,GSM2306086,GSM2306086: NICD rep2; Danio rerio; RNA Seq,GSM2306086,,1,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2306086,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP087617,,,mutant2.fastq.gz,fastq,1745551857.0,34226507.0,GSM2306086 r1,0:51 1:0,A:414724753;C:449494336;G:403529006;T:477747391;N:56371,51,0,,,414724753,449494336,403529006,477747391,56371,SRX2148086,SRS1679264,SRA464955,GEO,Stowers Institute for Medical Research,1,0.77355,,0.08842,,0.71674,,0.48589,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2016-09-08,Pharyngula,Embryo,Tail,Multi-system
41314,SRR4199305,SRX2148085,SRS1679263,SRP087617,PRJNA342262,Proliferation independent regulation of organ size by Notch signaling,GSE86571,Transcriptome Analysis,Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow  we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails  with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate  using HiSeq 2500 Illumina.,,pubmed:28085667,,NICD rep1,GSM2306085,,source name:dissociated embryo tails|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf,NICD rep1,Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters  p 8   transcriptome index  G  o   no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters  p 4  g  o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters  m intersection nonempty  s no  f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample  one includes FPKM values for each Sample.,dissociated embryo tails,Zebrafish embryos positive for GFP were selected.,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.,strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf,GSM2306085,GSM2306085: NICD rep1; Danio rerio; RNA Seq,GSM2306085,,1,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2306085,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP087617,,,mutant1.fastq.gz,fastq,1606289064.0,31495864.0,GSM2306085 r1,0:51 1:0,A:383363329;C:409816147;G:373853062;T:439205035;N:51491,51,0,,,383363329,409816147,373853062,439205035,51491,SRX2148085,SRS1679263,SRA464955,GEO,Stowers Institute for Medical Research,1,0.80199,,0.09405,,0.71382,,0.48651,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2016-09-08,Pharyngula,Embryo,Tail,Multi-system
41315,SRR4199304,SRX2148084,SRS1679262,SRP087617,PRJNA342262,Proliferation independent regulation of organ size by Notch signaling,GSE86571,Transcriptome Analysis,Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow  we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails  with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate  using HiSeq 2500 Illumina.,,pubmed:28085667,,WT rep3,GSM2306084,,source name:dissociated embryo tails|strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type,WT rep3,Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters  p 8   transcriptome index  G  o   no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters  p 4  g  o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters  m intersection nonempty  s no  f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample  one includes FPKM values for each Sample.,dissociated embryo tails,Zebrafish embryos positive for GFP were selected.,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.,strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type,GSM2306084,GSM2306084: WT rep3; Danio rerio; RNA Seq,GSM2306084,,1,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2306084,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP087617,,,WT3.fastq.gz,fastq,1621399650.0,31792150.0,GSM2306084 r1,0:51 1:0,A:394689371;C:400826196;G:384059217;T:441773624;N:51242,51,0,,,394689371,400826196,384059217,441773624,51242,SRX2148084,SRS1679262,SRA464955,GEO,Stowers Institute for Medical Research,1,0.87053,,0.08236,,0.7218,,0.4831,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2016-09-08,Pharyngula,Embryo,Tail,Multi-system
41316,SRR4199303,SRX2148083,SRS1679261,SRP087617,PRJNA342262,Proliferation independent regulation of organ size by Notch signaling,GSE86571,Transcriptome Analysis,Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow  we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails  with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate  using HiSeq 2500 Illumina.,,pubmed:28085667,,WT rep2,GSM2306083,,source name:dissociated embryo tails|strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type,WT rep2,Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters  p 8   transcriptome index  G  o   no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters  p 4  g  o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters  m intersection nonempty  s no  f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample  one includes FPKM values for each Sample.,dissociated embryo tails,Zebrafish embryos positive for GFP were selected.,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.,strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type,GSM2306083,GSM2306083: WT rep2; Danio rerio; RNA Seq,GSM2306083,,1,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2306083,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP087617,,,WT2.fastq.gz,fastq,1626903774.0,31900074.0,GSM2306083 r1,0:51 1:0,A:394214874;C:407655291;G:379120984;T:445859413;N:53212,51,0,,,394214874,407655291,379120984,445859413,53212,SRX2148083,SRS1679261,SRA464955,GEO,Stowers Institute for Medical Research,1,0.81975,,0.09539,,0.70869,,0.4872,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2016-09-08,Pharyngula,Embryo,Tail,Multi-system
41317,SRR4199302,SRX2148082,SRS1679260,SRP087617,PRJNA342262,Proliferation independent regulation of organ size by Notch signaling,GSE86571,Transcriptome Analysis,Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow  we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails  with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate  using HiSeq 2500 Illumina.,,pubmed:28085667,,WT rep1,GSM2306082,,source name:dissociated embryo tails|strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type,WT rep1,Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters  p 8   transcriptome index  G  o   no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters  p 4  g  o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters  m intersection nonempty  s no  f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample  one includes FPKM values for each Sample.,dissociated embryo tails,Zebrafish embryos positive for GFP were selected.,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.,strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type,GSM2306082,GSM2306082: WT rep1; Danio rerio; RNA Seq,GSM2306082,,1,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2306082,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP087617,,,WT1.fastq.gz,fastq,1646867622.0,32291522.0,GSM2306082 r1,0:51 1:0,A:400030238;C:412959654;G:377713613;T:456111038;N:53079,51,0,,,400030238,412959654,377713613,456111038,53079,SRX2148082,SRS1679260,SRA464955,GEO,Stowers Institute for Medical Research,1,0.81411,,0.10419,,0.70621,,0.48075,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2016-09-08,Pharyngula,Embryo,Tail,Multi-system
41363,SRR4369389,SRX2224020,SRS1731682,SRP090938,PRJNA345605,Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal,GSE87704,Transcriptome Analysis,We report the transcriptional response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis  storage  and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER  where lipids are formed and assigned to their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.,,pubmed:27655916,,4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep3,GSM2339156,,source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep3,Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.,digestive organs intestine  liver  pancreas of 10 zebrafish larvae,Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM,strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,GSM2339156,GSM2339156: 4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep3; Danio rerio; RNA Seq,GSM2339156,,1,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,GEO Accession:GSM2339156,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP090938,,,EZ243.fq.gz,fastq,1057994900.0,21159898.0,GSM2339156 r1,0:50,A:280437817;C:246195249;G:248543608;T:282775343;N:42883,50,,,,280437817,246195249,248543608,282775343,42883,SRX2224020,SRS1731682,SRA482638,GEO,"Yixian Zheng, Embryology, Carnegie Institution for Science",1,0.92441,,0.07101,,0.73259,,0.53564,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-10-06,Larval,Larval,Multi-tissue,Multi-system
41364,SRR4369388,SRX2224018,SRS1731680,SRP090938,PRJNA345605,Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal,GSE87704,Transcriptome Analysis,We report the transcriptional response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis  storage  and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER  where lipids are formed and assigned to their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.,,pubmed:27655916,,1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep3,GSM2339155,,source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep3,Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.,digestive organs intestine  liver  pancreas of 10 zebrafish larvae,Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM,strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,GSM2339155,GSM2339155: 1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep3; Danio rerio; RNA Seq,GSM2339155,,1,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,GEO Accession:GSM2339155,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP090938,,,EZ213.fq.gz,fastq,1192895250.0,23857905.0,GSM2339155 r1,0:50,A:311520729;C:281518333;G:288563950;T:311243358;N:48880,50,,,,311520729,281518333,288563950,311243358,48880,SRX2224018,SRS1731680,SRA482638,GEO,"Yixian Zheng, Embryology, Carnegie Institution for Science",1,0.92622,,0.06398,,0.7315,,0.51969,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-10-06,Larval,Larval,Multi-tissue,Multi-system
41365,SRR4369387,SRX2224017,SRS1731679,SRP090938,PRJNA345605,Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal,GSE87704,Transcriptome Analysis,We report the transcriptional response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis  storage  and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER  where lipids are formed and assigned to their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.,,pubmed:27655916,,Unfed 6.5 dpf zebrafish larvae low fat cohort rep3,GSM2339154,,source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,Unfed 6.5 dpf zebrafish larvae low fat cohort rep3,Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.,digestive organs intestine  liver  pancreas of 10 zebrafish larvae,Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM,strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,GSM2339154,GSM2339154: Unfed 6.5 dpf zebrafish larvae low fat cohort rep3; Danio rerio; RNA Seq,GSM2339154,,1,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,GEO Accession:GSM2339154,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP090938,,,EZ203.fq.gz,fastq,1333885750.0,26677715.0,GSM2339154 r1,0:50,A:350227472;C:314164789;G:317046609;T:352393122;N:53758,50,,,,350227472,314164789,317046609,352393122,53758,SRX2224017,SRS1731679,SRA482638,GEO,"Yixian Zheng, Embryology, Carnegie Institution for Science",1,0.92695,,0.07507,,0.72675,,0.54558,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-10-06,Larval,Larval,Multi-tissue,Multi-system
41366,SRR4369386,SRX2224016,SRS1731677,SRP090938,PRJNA345605,Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal,GSE87704,Transcriptome Analysis,We report the transcriptional response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis  storage  and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER  where lipids are formed and assigned to their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.,,pubmed:27655916,,4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3,GSM2339153,,source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3,Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.,digestive organs intestine  liver  pancreas of 10 zebrafish larvae,Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM,strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,GSM2339153,GSM2339153: 4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3; Danio rerio; RNA Seq,GSM2339153,,1,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,GEO Accession:GSM2339153,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP090938,,,EZ143.fq.gz,fastq,3620501750.0,72410035.0,GSM2339153 r1,0:50,A:928100369;C:870292711;G:888545580;T:933466612;N:96478,50,,,,928100369,870292711,888545580,933466612,96478,SRX2224016,SRS1731677,SRA482638,GEO,"Yixian Zheng, Embryology, Carnegie Institution for Science",1,0.93833,,0.05511,,0.75032,,0.55771,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-10-06,Larval,Larval,Multi-tissue,Multi-system
41367,SRR4369385,SRX2224015,SRS1731678,SRP090938,PRJNA345605,Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal,GSE87704,Transcriptome Analysis,We report the transcriptional response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis  storage  and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER  where lipids are formed and assigned to their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.,,pubmed:27655916,,1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3,GSM2339152,,source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3,Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.,digestive organs intestine  liver  pancreas of 10 zebrafish larvae,Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM,strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,GSM2339152,GSM2339152: 1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3; Danio rerio; RNA Seq,GSM2339152,,1,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,GEO Accession:GSM2339152,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP090938,,,EZ113.fq.gz,fastq,2177871950.0,43557439.0,GSM2339152 r1,0:50,A:563893287;C:522092755;G:523081504;T:568747495;N:56909,50,,,,563893287,522092755,523081504,568747495,56909,SRX2224015,SRS1731678,SRA482638,GEO,"Yixian Zheng, Embryology, Carnegie Institution for Science",1,0.93698,,0.06235,,0.75335,,0.53049,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-10-06,Larval,Larval,Multi-tissue,Multi-system
41368,SRR4369384,SRX2224014,SRS1731676,SRP090938,PRJNA345605,Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal,GSE87704,Transcriptome Analysis,We report the transcriptional response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis  storage  and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER  where lipids are formed and assigned to their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.,,pubmed:27655916,,Unfed 6.5 dpf zebrafish larvae high fat cohort rep3,GSM2339151,,source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,Unfed 6.5 dpf zebrafish larvae high fat cohort rep3,Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.,digestive organs intestine  liver  pancreas of 10 zebrafish larvae,Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM,strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,GSM2339151,GSM2339151: Unfed 6.5 dpf zebrafish larvae high fat cohort rep3; Danio rerio; RNA Seq,GSM2339151,,1,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,GEO Accession:GSM2339151,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP090938,,,EZ103.fq.gz,fastq,1451132900.0,29022658.0,GSM2339151 r1,0:50,A:377007117;C:346007409;G:346873642;T:381206074;N:38658,50,,,,377007117,346007409,346873642,381206074,38658,SRX2224014,SRS1731676,SRA482638,GEO,"Yixian Zheng, Embryology, Carnegie Institution for Science",1,0.93743,,0.06292,,0.74241,,0.53805,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-10-06,Larval,Larval,Multi-tissue,Multi-system
41369,SRR4369383,SRX2224013,SRS1731675,SRP090938,PRJNA345605,Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal,GSE87704,Transcriptome Analysis,We report the transcriptional response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis  storage  and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER  where lipids are formed and assigned to their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.,,pubmed:27655916,,4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep2,GSM2339150,,source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep2,Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.,digestive organs intestine  liver  pancreas of 10 zebrafish larvae,Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM,strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,GSM2339150,GSM2339150: 4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep2; Danio rerio; RNA Seq,GSM2339150,,1,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,GEO Accession:GSM2339150,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP090938,,,EZ242.fq.gz,fastq,1989936500.0,39798730.0,GSM2339150 r1,0:50,A:523392551;C:467800437;G:470494505;T:528201420;N:47587,50,,,,523392551,467800437,470494505,528201420,47587,SRX2224013,SRS1731675,SRA482638,GEO,"Yixian Zheng, Embryology, Carnegie Institution for Science",1,0.93233,,0.07279,,0.72987,,0.54632,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-10-06,Larval,Larval,Multi-tissue,Multi-system
41370,SRR4369382,SRX2224012,SRS1731674,SRP090938,PRJNA345605,Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal,GSE87704,Transcriptome Analysis,We report the transcriptional response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis  storage  and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER  where lipids are formed and assigned to their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.,,pubmed:27655916,,1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep2,GSM2339149,,source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep2,Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.,digestive organs intestine  liver  pancreas of 10 zebrafish larvae,Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM,strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,GSM2339149,GSM2339149: 1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep2; Danio rerio; RNA Seq,GSM2339149,,1,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,GEO Accession:GSM2339149,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP090938,,,EZ212.fq.gz,fastq,2625058500.0,52501170.0,GSM2339149 r1,0:50,A:685255578;C:619614827;G:635559034;T:684566225;N:62836,50,,,,685255578,619614827,635559034,684566225,62836,SRX2224012,SRS1731674,SRA482638,GEO,"Yixian Zheng, Embryology, Carnegie Institution for Science",1,0.93545,,0.06765,,0.74399,,0.53905,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-10-06,Larval,Larval,Multi-tissue,Multi-system
41371,SRR4369381,SRX2224011,SRS1731672,SRP090938,PRJNA345605,Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal,GSE87704,Transcriptome Analysis,We report the transcriptional response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis  storage  and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER  where lipids are formed and assigned to their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.,,pubmed:27655916,,Unfed 6.5 dpf zebrafish larvae low fat cohort rep2,GSM2339148,,source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,Unfed 6.5 dpf zebrafish larvae low fat cohort rep2,Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.,digestive organs intestine  liver  pancreas of 10 zebrafish larvae,Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM,strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,GSM2339148,GSM2339148: Unfed 6.5 dpf zebrafish larvae low fat cohort rep2; Danio rerio; RNA Seq,GSM2339148,,1,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,GEO Accession:GSM2339148,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP090938,,,EZ202.fq.gz,fastq,1339075850.0,26781517.0,GSM2339148 r1,0:50,A:350406690;C:316421667;G:317254683;T:354961605;N:31205,50,,,,350406690,316421667,317254683,354961605,31205,SRX2224011,SRS1731672,SRA482638,GEO,"Yixian Zheng, Embryology, Carnegie Institution for Science",1,0.93323,,0.07254,,0.7307,,0.55068,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-10-06,Larval,Larval,Multi-tissue,Multi-system
41372,SRR4369380,SRX2224010,SRS1731671,SRP090938,PRJNA345605,Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal,GSE87704,Transcriptome Analysis,We report the transcriptional response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis  storage  and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER  where lipids are formed and assigned to their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.,,pubmed:27655916,,4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep2,GSM2339147,,source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep2,Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.,digestive organs intestine  liver  pancreas of 10 zebrafish larvae,Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM,strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,GSM2339147,GSM2339147: 4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep2; Danio rerio; RNA Seq,GSM2339147,,1,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,GEO Accession:GSM2339147,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP090938,,,EZ142.fq.gz,fastq,1286162750.0,25723255.0,GSM2339147 r1,0:50,A:346299275;C:294122420;G:300696019;T:345003487;N:41549,50,,,,346299275,294122420,300696019,345003487,41549,SRX2224010,SRS1731671,SRA482638,GEO,"Yixian Zheng, Embryology, Carnegie Institution for Science",1,0.9281,,0.07755,,0.7305,,0.53462,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-10-06,Larval,Larval,Multi-tissue,Multi-system
41373,SRR4369379,SRX2224009,SRS1731673,SRP090938,PRJNA345605,Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal,GSE87704,Transcriptome Analysis,We report the transcriptional response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis  storage  and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER  where lipids are formed and assigned to their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.,,pubmed:27655916,,1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep2,GSM2339146,,source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep2,Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.,digestive organs intestine  liver  pancreas of 10 zebrafish larvae,Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM,strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf,GSM2339146,GSM2339146: 1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep2; Danio rerio; RNA Seq,GSM2339146,,1,At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at  80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.,GEO Accession:GSM2339146,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP090938,,,EZ112.fq.gz,fastq,2002111100.0,40042222.0,GSM2339146 r1,0:50,A:528562099;C:471825161;G:473013263;T:528647491;N:63086,50,,,,528562099,471825161,473013263,528647491,63086,SRX2224009,SRS1731673,SRA482638,GEO,"Yixian Zheng, Embryology, Carnegie Institution for Science",1,0.93335,,0.07285,,0.7419,,0.54916,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-10-06,Larval,Larval,Multi-tissue,Multi-system