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542 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue_curation_coarse = "Multi-system"

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experiment.library_selection 7

devstage_curation 5

devstage_curation_coarse 4

experiment.platform 3

experiment.library_strategy 3

tissue_curation 2

tissue_curation_coarse 1

  • Multi-system · 542 ✖

technology 1

  • unknown · 542 ✖

experiment.library_source 1

experiment.library_layout 1

  • SINGLE · 542 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
51 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
168 168 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
169 169 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
170 170 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
175 175 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
181 181 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 …     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 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 …     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 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 …     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 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 000rc…   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 000rc… 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 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 000rc…   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 000rc… 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 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 000rc…   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 000rc… 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 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 000rc…   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 000rc… 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 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 000rc…   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 000rc… 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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