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156 rows where experiment.library_selection = "cDNA", technology = "smartseq" and tissue_curation_coarse = "Sensory System"

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devstage_curation_coarse 3

devstage_curation 3

tissue_curation 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Sensory System · 156 ✖

technology 1

  • smartseq · 156 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • cDNA · 156 ✖
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
30572 30572 SRR27848813 SRX23511754 SRS20362222 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Wildtype 7 GSM8061015   source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing Wildtype 7 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Wildtype GSM8061015 GSM8061015: Wildtype 7; Danio rerio; RNA Seq GSM8061015 r1 GSM8061015 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py WT7_1.fq.gz WT7_2.fq.gz fastq fastq 16387213200.0 54624044.0 GSM8061015 r1 0:150 1:150 A:4787207224;C:3312386758;G:3384738324;T:4902574775;N:306119 150 150     4787207224 3312386758 3384738324 4902574775 306119 SRX23511754 SRS20362222 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.92431 0.91825 0.16903 0.16976 0.74067 0.75189 0.50167 0.50261 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30573 30573 SRR27848814 SRX23511753 SRS20362221 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Wildtype 6 GSM8061014   source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing Wildtype 6 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Wildtype GSM8061014 GSM8061014: Wildtype 6; Danio rerio; RNA Seq GSM8061014 r1 GSM8061014 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py WT6_1.fq.gz WT6_2.fq.gz fastq fastq 19114278900.0 63714263.0 GSM8061014 r1 0:150 1:150 A:5885874877;C:3513555230;G:3610119151;T:6104379853;N:349789 150 150     5885874877 3513555230 3610119151 6104379853 349789 SRX23511753 SRS20362221 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.88104 0.87237 0.33066 0.33508 0.7357 0.7499 0.52706 0.51369 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30574 30574 SRR27848815 SRX23511752 SRS20362220 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Wildtype 5 GSM8061013   source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing Wildtype 5 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Wildtype GSM8061013 GSM8061013: Wildtype 5; Danio rerio; RNA Seq GSM8061013 r1 GSM8061013 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py WT5_2.fq.gz WT5_1.fq.gz fastq fastq 16120305900.0 53734353.0 GSM8061013 r1 0:150 1:150 A:4774586081;C:3152393582;G:3245217813;T:4947808687;N:299737 150 150     4774586081 3152393582 3245217813 4947808687 299737 SRX23511752 SRS20362220 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.90351 0.89372 0.19598 0.19188 0.74468 0.76037 0.49643 0.5012 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30575 30575 SRR27848816 SRX23511751 SRS20362219 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Wildtype 4 GSM8061012   source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing Wildtype 4 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Wildtype GSM8061012 GSM8061012: Wildtype 4; Danio rerio; RNA Seq GSM8061012 r1 GSM8061012 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py WT4_1.fq.gz WT4_2.fq.gz fastq fastq 15545813700.0 51819379.0 GSM8061012 r1 0:150 1:150 A:4735339999;C:2883223993;G:2979819364;T:4947148649;N:281695 150 150     4735339999 2883223993 2979819364 4947148649 281695 SRX23511751 SRS20362219 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.88431 0.87409 0.2472 0.24596 0.74675 0.76534 0.50472 0.51348 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30576 30576 SRR27848817 SRX23511750 SRS20362218 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Wildtype 3 GSM8061011   source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing Wildtype 3 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Wildtype GSM8061011 GSM8061011: Wildtype 3; Danio rerio; RNA Seq GSM8061011 r1 GSM8061011 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py WT3_1.fq.gz WT3_2.fq.gz fastq fastq 17883593700.0 59611979.0 GSM8061011 r1 0:150 1:150 A:5305029339;C:3503937995;G:3594774195;T:5479523425;N:328746 150 150     5305029339 3503937995 3594774195 5479523425 328746 SRX23511750 SRS20362218 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.90376 0.89786 0.22127 0.22019 0.72941 0.74257 0.49283 0.4977 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30577 30577 SRR27848818 SRX23511749 SRS20362217 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Wildtype 2 GSM8061010   source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing Wildtype 2 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Wildtype GSM8061010 GSM8061010: Wildtype 2; Danio rerio; RNA Seq GSM8061010 r1 GSM8061010 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py WT2_1.fq.gz WT2_2.fq.gz fastq fastq 15921002400.0 53070008.0 GSM8061010 r1 0:150 1:150 A:4801739158;C:2898179014;G:3037454009;T:5183338180;N:292039 150 150     4801739158 2898179014 3037454009 5183338180 292039 SRX23511749 SRS20362217 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.88935 0.87616 0.22376 0.2085 0.75367 0.78123 0.53443 0.51122 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30578 30578 SRR27848819 SRX23511748 SRS20362216 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Wildtype 1 GSM8061009   source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing Wildtype 1 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Wildtype GSM8061009 GSM8061009: Wildtype 1; Danio rerio; RNA Seq GSM8061009 r1 GSM8061009 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py WT1_1.fq.gz WT1_2.fq.gz fastq fastq 15664926900.0 52216423.0 GSM8061009 r1 0:150 1:150 A:4654413024;C:3082161368;G:3150203371;T:4777859952;N:289185 150 150     4654413024 3082161368 3150203371 4777859952 289185 SRX23511748 SRS20362216 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.9012 0.89646 0.22096 0.21863 0.73507 0.7475 0.4816 0.4726 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30579 30579 SRR27848820 SRX23511747 SRS20362215 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Choroideremia 7 GSM8061008   source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing Choroideremia 7 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Choroideremia GSM8061008 GSM8061008: Choroideremia 7; Danio rerio; RNA Seq GSM8061008 r1 GSM8061008 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py CHM7_2.fq.gz CHM7_1.fq.gz fastq fastq 16991281200.0 56637604.0 GSM8061008 r1 0:150 1:150 A:4896856485;C:3497447652;G:3598783228;T:4998138764;N:55071 150 150     4896856485 3497447652 3598783228 4998138764 55071 SRX23511747 SRS20362215 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.926 0.92518 0.16779 0.16551 0.72393 0.73513 0.51723 0.51214 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30580 30580 SRR27848821 SRX23511746 SRS20362214 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Choroideremia 6 GSM8061007   source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing Choroideremia 6 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Choroideremia GSM8061007 GSM8061007: Choroideremia 6; Danio rerio; RNA Seq GSM8061007 r1 GSM8061007 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py CHM6_1.fq.gz CHM6_2.fq.gz fastq fastq 18881901900.0 62939673.0 GSM8061007 r1 0:150 1:150 A:5796692721;C:3348140904;G:3547934333;T:6189072751;N:61191 150 150     5796692721 3348140904 3547934333 6189072751 61191 SRX23511746 SRS20362214 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.86869 0.86484 0.26053 0.2569 0.75057 0.77705 0.66121 0.65975 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30581 30581 SRR27848822 SRX23511745 SRS20362213 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Choroideremia 5 GSM8061006   source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing Choroideremia 5 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Choroideremia GSM8061006 GSM8061006: Choroideremia 5; Danio rerio; RNA Seq GSM8061006 r1 GSM8061006 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py CHM5_2.fq.gz CHM5_1.fq.gz fastq fastq 17802156900.0 59340523.0 GSM8061006 r1 0:150 1:150 A:5198674613;C:3599354426;G:3698229931;T:5305840019;N:57911 150 150     5198674613 3599354426 3698229931 5305840019 57911 SRX23511745 SRS20362213 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.9109 0.91251 0.18901 0.18793 0.72354 0.73456 0.51839 0.52348 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30582 30582 SRR27848823 SRX23511744 SRS20362212 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Choroideremia 4 GSM8061005   source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing Choroideremia 4 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Choroideremia GSM8061005 GSM8061005: Choroideremia 4; Danio rerio; RNA Seq GSM8061005 r1 GSM8061005 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py CHM4_2.fq.gz CHM4_1.fq.gz fastq fastq 15944831400.0 53149438.0 GSM8061005 r1 0:150 1:150 A:4833633886;C:2870981386;G:3055307522;T:5184819306;N:89300 150 150     4833633886 2870981386 3055307522 5184819306 89300 SRX23511744 SRS20362212 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.88929 0.88364 0.25277 0.24996 0.75317 0.77826 0.64914 0.65907 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30583 30583 SRR27848824 SRX23511743 SRS20362211 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Choroideremia 3 GSM8061004   source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing Choroideremia 3 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Choroideremia GSM8061004 GSM8061004: Choroideremia 3; Danio rerio; RNA Seq GSM8061004 r1 GSM8061004 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py CHM3_1.fq.gz CHM3_2.fq.gz fastq fastq 16028608800.0 53428696.0 GSM8061004 r1 0:150 1:150 A:4842495383;C:2966448486;G:3084331699;T:5135033798;N:299434 150 150     4842495383 2966448486 3084331699 5135033798 299434 SRX23511743 SRS20362211 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.89747 0.88445 0.23706 0.23597 0.72904 0.75187 0.5514 0.45471 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30584 30584 SRR27848825 SRX23511742 SRS20362210 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Choroideremia 2 GSM8061003   source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing Choroideremia 2 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Choroideremia GSM8061003 GSM8061003: Choroideremia 2; Danio rerio; RNA Seq GSM8061003 r1 GSM8061003 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py CHM2_1.fq.gz CHM2_2.fq.gz fastq fastq 14968884300.0 49896281.0 GSM8061003 r1 0:150 1:150 A:4575866591;C:2606132581;G:2819446784;T:4967389772;N:48572 150 150     4575866591 2606132581 2819446784 4967389772 48572 SRX23511742 SRS20362210 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.88022 0.87326 0.29312 0.29812 0.7335 0.76228 0.5854 0.57614 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30585 30585 SRR27848826 SRX23511741 SRS20362209 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Choroideremia 1 GSM8061002   source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing Choroideremia 1 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Choroideremia GSM8061002 GSM8061002: Choroideremia 1; Danio rerio; RNA Seq GSM8061002 r1 GSM8061002 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py CHM1_2.fq.gz CHM1_1.fq.gz fastq fastq 15862639500.0 52875465.0 GSM8061002 r1 0:150 1:150 A:4812544148;C:2881706406;G:3014671171;T:5153419977;N:297798 150 150     4812544148 2881706406 3014671171 5153419977 297798 SRX23511741 SRS20362209 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.89157 0.87804 0.24616 0.24284 0.73884 0.76232 0.58251 0.58918 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
34807 34807 SRR32289929 SRX27626974 SRS24034243 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 14dpi biological replicate 6 GSM8784941   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 14dpi biological replicate 6 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784941 GSM8784941: FAC sorted RGCs at 14dpi biological replicate 6; Danio rerio; RNA Seq GSM8784941 r1 GSM8784941 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122375.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 455140014.0 8924314.0 GSM8784941 r1 0:51 A:121395551;C:104372745;G:106322577;T:123006247;N:42894 51       121395551 104372745 106322577 123006247 42894 SRX27626974 SRS24034243 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34808 34808 SRR32289930 SRX27626974 SRS24034243 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 14dpi biological replicate 6 GSM8784941   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 14dpi biological replicate 6 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784941 GSM8784941: FAC sorted RGCs at 14dpi biological replicate 6; Danio rerio; RNA Seq GSM8784941 r1 GSM8784941 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122375.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 466246080.0 9142080.0 GSM8784941 r2 0:51 A:124363664;C:106868642;G:108780226;T:126189949;N:43599 51       124363664 106868642 108780226 126189949 43599 SRX27626974 SRS24034243 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34809 34809 SRR32289931 SRX27626973 SRS24034241 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 14dpi biological replicate 5 GSM8784940   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 14dpi biological replicate 5 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784940 GSM8784940: FAC sorted RGCs at 14dpi biological replicate 5; Danio rerio; RNA Seq GSM8784940 r1 GSM8784940 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121325.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 453422589.0 8890639.0 GSM8784940 r1 0:51 A:119318402;C:105882527;G:107813042;T:120365525;N:43093 51       119318402 105882527 107813042 120365525 43093 SRX27626973 SRS24034241 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34810 34810 SRR32289932 SRX27626973 SRS24034241 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 14dpi biological replicate 5 GSM8784940   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 14dpi biological replicate 5 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784940 GSM8784940: FAC sorted RGCs at 14dpi biological replicate 5; Danio rerio; RNA Seq GSM8784940 r1 GSM8784940 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121325.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 464612040.0 9110040.0 GSM8784940 r2 0:51 A:122313464;C:108440796;G:110356081;T:123457974;N:43725 51       122313464 108440796 110356081 123457974 43725 SRX27626973 SRS24034241 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34811 34811 SRR32289933 SRX27626972 SRS24034242 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 14dpi biological replicate 4 GSM8784939   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 14dpi biological replicate 4 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784939 GSM8784939: FAC sorted RGCs at 14dpi biological replicate 4; Danio rerio; RNA Seq GSM8784939 r1 GSM8784939 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121324.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 399194493.0 7827343.0 GSM8784939 r1 0:51 A:104203040;C:94204942;G:95935068;T:104813749;N:37694 51       104203040 94204942 95935068 104813749 37694 SRX27626972 SRS24034242 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34812 34812 SRR32289934 SRX27626972 SRS24034242 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 14dpi biological replicate 4 GSM8784939   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 14dpi biological replicate 4 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784939 GSM8784939: FAC sorted RGCs at 14dpi biological replicate 4; Danio rerio; RNA Seq GSM8784939 r1 GSM8784939 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121324.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 407414775.0 7988525.0 GSM8784939 r2 0:51 A:106355289;C:96099106;G:97825197;T:107096823;N:38360 51       106355289 96099106 97825197 107096823 38360 SRX27626972 SRS24034242 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34813 34813 SRR32289935 SRX27626971 SRS24034240 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 14dpi biological replicate 3 GSM8784938   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 14dpi biological replicate 3 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784938 GSM8784938: FAC sorted RGCs at 14dpi biological replicate 3; Danio rerio; RNA Seq GSM8784938 r1 GSM8784938 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121323.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 393819042.0 7721942.0 GSM8784938 r1 0:51 A:104716428;C:90712029;G:92875673;T:105476998;N:37914 51       104716428 90712029 92875673 105476998 37914 SRX27626971 SRS24034240 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34814 34814 SRR32289936 SRX27626971 SRS24034240 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 14dpi biological replicate 3 GSM8784938   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 14dpi biological replicate 3 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784938 GSM8784938: FAC sorted RGCs at 14dpi biological replicate 3; Danio rerio; RNA Seq GSM8784938 r1 GSM8784938 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121323.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 404191065.0 7925315.0 GSM8784938 r2 0:51 A:107484459;C:93060010;G:95238340;T:108369497;N:38759 51       107484459 93060010 95238340 108369497 38759 SRX27626971 SRS24034240 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34815 34815 SRR32289937 SRX27626970 SRS24034239 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 14dpi biological replicate 2 GSM8784937   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 14dpi biological replicate 2 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784937 GSM8784937: FAC sorted RGCs at 14dpi biological replicate 2; Danio rerio; RNA Seq GSM8784937 r1 GSM8784937 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121322.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 387042774.0 7589074.0 GSM8784937 r1 0:51 A:107517102;C:84333044;G:85962742;T:109191597;N:38289 51       107517102 84333044 85962742 109191597 38289 SRX27626970 SRS24034239 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34816 34816 SRR32289938 SRX27626970 SRS24034239 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 14dpi biological replicate 2 GSM8784937   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 14dpi biological replicate 2 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784937 GSM8784937: FAC sorted RGCs at 14dpi biological replicate 2; Danio rerio; RNA Seq GSM8784937 r1 GSM8784937 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121322.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 399657012.0 7836412.0 GSM8784937 r2 0:51 A:111048661;C:86998697;G:88636677;T:112933522;N:39455 51       111048661 86998697 88636677 112933522 39455 SRX27626970 SRS24034239 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34817 34817 SRR32289939 SRX27626969 SRS24034236 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 14dpi biological replicate 1 GSM8784936   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 14dpi biological replicate 1 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784936 GSM8784936: FAC sorted RGCs at 14dpi biological replicate 1; Danio rerio; RNA Seq GSM8784936 r1 GSM8784936 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121320.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 358289280.0 7025280.0 GSM8784936 r1 0:51 A:101071342;C:75109849;G:76553150;T:105519857;N:35082 51       101071342 75109849 76553150 105519857 35082 SRX27626969 SRS24034236 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34818 34818 SRR32289940 SRX27626969 SRS24034236 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 14dpi biological replicate 1 GSM8784936   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 14dpi biological replicate 1 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784936 GSM8784936: FAC sorted RGCs at 14dpi biological replicate 1; Danio rerio; RNA Seq GSM8784936 r1 GSM8784936 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121320.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 370202625.0 7258875.0 GSM8784936 r2 0:51 A:104421674;C:77537410;G:79038293;T:109169570;N:35678 51       104421674 77537410 79038293 109169570 35678 SRX27626969 SRS24034236 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34819 34819 SRR32289941 SRX27626968 SRS24034237 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 10dpi biological replicate 5 GSM8784935   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 10dpi biological replicate 5 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784935 GSM8784935: FAC sorted RGCs at 10dpi biological replicate 5; Danio rerio; RNA Seq GSM8784935 r1 GSM8784935 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122374.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 403359306.0 7909006.0 GSM8784935 r1 0:51 A:104505636;C:95925686;G:97605050;T:105285164;N:37770 51       104505636 95925686 97605050 105285164 37770 SRX27626968 SRS24034237 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34820 34820 SRR32289942 SRX27626968 SRS24034237 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 10dpi biological replicate 5 GSM8784935   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 10dpi biological replicate 5 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784935 GSM8784935: FAC sorted RGCs at 10dpi biological replicate 5; Danio rerio; RNA Seq GSM8784935 r1 GSM8784935 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122374.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 411821124.0 8074924.0 GSM8784935 r2 0:51 A:106698116;C:97949900;G:99548706;T:107586633;N:37769 51       106698116 97949900 99548706 107586633 37769 SRX27626968 SRS24034237 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34821 34821 SRR32289943 SRX27626967 SRS24034233 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 10dpi biological replicate 4 GSM8784934   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 10dpi biological replicate 4 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784934 GSM8784934: FAC sorted RGCs at 10dpi biological replicate 4; Danio rerio; RNA Seq GSM8784934 r1 GSM8784934 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121319.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 320645415.0 6287165.0 GSM8784934 r1 0:51 A:83667318;C:75715675;G:77201096;T:84031268;N:30058 51       83667318 75715675 77201096 84031268 30058 SRX27626967 SRS24034233 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34822 34822 SRR32289944 SRX27626967 SRS24034233 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 10dpi biological replicate 4 GSM8784934   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 10dpi biological replicate 4 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784934 GSM8784934: FAC sorted RGCs at 10dpi biological replicate 4; Danio rerio; RNA Seq GSM8784934 r1 GSM8784934 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121319.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 326655969.0 6405019.0 GSM8784934 r2 0:51 A:85253239;C:77113202;G:78588132;T:85671193;N:30203 51       85253239 77113202 78588132 85671193 30203 SRX27626967 SRS24034233 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34823 34823 SRR32289945 SRX27626966 SRS24034235 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 10dpi biological replicate 3 GSM8784933   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 10dpi biological replicate 3 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784933 GSM8784933: FAC sorted RGCs at 10dpi biological replicate 3; Danio rerio; RNA Seq GSM8784933 r1 GSM8784933 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121318.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 383772552.0 7524952.0 GSM8784933 r1 0:51 A:100725108;C:90120177;G:92143732;T:100747122;N:36413 51       100725108 90120177 92143732 100747122 36413 SRX27626966 SRS24034235 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34824 34824 SRR32289946 SRX27626966 SRS24034235 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 10dpi biological replicate 3 GSM8784933   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 10dpi biological replicate 3 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784933 GSM8784933: FAC sorted RGCs at 10dpi biological replicate 3; Danio rerio; RNA Seq GSM8784933 r1 GSM8784933 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121318.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 392096007.0 7688157.0 GSM8784933 r2 0:51 A:102939588;C:92028680;G:94033209;T:103058157;N:36373 51       102939588 92028680 94033209 103058157 36373 SRX27626966 SRS24034235 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34825 34825 SRR32289947 SRX27626965 SRS24034238 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 10dpi biological replicate 2 GSM8784932   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 10dpi biological replicate 2 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784932 GSM8784932: FAC sorted RGCs at 10dpi biological replicate 2; Danio rerio; RNA Seq GSM8784932 r1 GSM8784932 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121317.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 396699216.0 7778416.0 GSM8784932 r1 0:51 A:103913407;C:93411140;G:95295922;T:104041015;N:37732 51       103913407 93411140 95295922 104041015 37732 SRX27626965 SRS24034238 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34826 34826 SRR32289948 SRX27626965 SRS24034238 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 10dpi biological replicate 2 GSM8784932   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 10dpi biological replicate 2 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784932 GSM8784932: FAC sorted RGCs at 10dpi biological replicate 2; Danio rerio; RNA Seq GSM8784932 r1 GSM8784932 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121317.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 407433696.0 7988896.0 GSM8784932 r2 0:51 A:106734482;C:95879695;G:97797451;T:106984011;N:38057 51       106734482 95879695 97797451 106984011 38057 SRX27626965 SRS24034238 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34827 34827 SRR32289949 SRX27626964 SRS24034232 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 10dpi biological replicate 1 GSM8784931   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 10dpi biological replicate 1 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784931 GSM8784931: FAC sorted RGCs at 10dpi biological replicate 1; Danio rerio; RNA Seq GSM8784931 r1 GSM8784931 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121316.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 357420852.0 7008252.0 GSM8784931 r1 0:51 A:100707954;C:76739501;G:77474055;T:102464781;N:34561 51       100707954 76739501 77474055 102464781 34561 SRX27626964 SRS24034232 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34828 34828 SRR32289950 SRX27626964 SRS24034232 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 10dpi biological replicate 1 GSM8784931   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 10dpi biological replicate 1 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784931 GSM8784931: FAC sorted RGCs at 10dpi biological replicate 1; Danio rerio; RNA Seq GSM8784931 r1 GSM8784931 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121316.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 369272181.0 7240631.0 GSM8784931 r2 0:51 A:104043292;C:79231475;G:79962686;T:105999425;N:35303 51       104043292 79231475 79962686 105999425 35303 SRX27626964 SRS24034232 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34829 34829 SRR32289951 SRX27626963 SRS24034234 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 6dpi biological replicate 5 GSM8784930   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 6dpi biological replicate 5 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784930 GSM8784930: FAC sorted RGCs at 6dpi biological replicate 5; Danio rerio; RNA Seq GSM8784930 r1 GSM8784930 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122373.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 383701101.0 7523551.0 GSM8784930 r1 0:51 A:101986811;C:88337442;G:89758931;T:103581971;N:35946 51       101986811 88337442 89758931 103581971 35946 SRX27626963 SRS24034234 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34830 34830 SRR32289952 SRX27626963 SRS24034234 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 6dpi biological replicate 5 GSM8784930   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 6dpi biological replicate 5 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784930 GSM8784930: FAC sorted RGCs at 6dpi biological replicate 5; Danio rerio; RNA Seq GSM8784930 r1 GSM8784930 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122373.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 394847355.0 7742105.0 GSM8784930 r2 0:51 A:104937168;C:90871625;G:92274823;T:106726849;N:36890 51       104937168 90871625 92274823 106726849 36890 SRX27626963 SRS24034234 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34831 34831 SRR32289953 SRX27626962 SRS24034230 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 6dpi biological replicate 4 GSM8784929   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 6dpi biological replicate 4 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784929 GSM8784929: FAC sorted RGCs at 6dpi biological replicate 4; Danio rerio; RNA Seq GSM8784929 r1 GSM8784929 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121313.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 397357269.0 7791319.0 GSM8784929 r1 0:51 A:102962865;C:94382913;G:96076584;T:103896489;N:38418 51       102962865 94382913 96076584 103896489 38418 SRX27626962 SRS24034230 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34832 34832 SRR32289954 SRX27626962 SRS24034230 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 6dpi biological replicate 4 GSM8784929   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 6dpi biological replicate 4 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784929 GSM8784929: FAC sorted RGCs at 6dpi biological replicate 4; Danio rerio; RNA Seq GSM8784929 r1 GSM8784929 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121313.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 407641317.0 7992967.0 GSM8784929 r2 0:51 A:105635966;C:96802890;G:98458161;T:106705494;N:38806 51       105635966 96802890 98458161 106705494 38806 SRX27626962 SRS24034230 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34833 34833 SRR32289955 SRX27626961 SRS24034228 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 6dpi biological replicate 3 GSM8784928   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 6dpi biological replicate 3 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784928 GSM8784928: FAC sorted RGCs at 6dpi biological replicate 3; Danio rerio; RNA Seq GSM8784928 r1 GSM8784928 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121312.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 375101328.0 7354928.0 GSM8784928 r1 0:51 A:98240052;C:88061621;G:89879822;T:98883790;N:36043 51       98240052 88061621 89879822 98883790 36043 SRX27626961 SRS24034228 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34834 34834 SRR32289956 SRX27626961 SRS24034228 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 6dpi biological replicate 3 GSM8784928   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 6dpi biological replicate 3 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784928 GSM8784928: FAC sorted RGCs at 6dpi biological replicate 3; Danio rerio; RNA Seq GSM8784928 r1 GSM8784928 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121312.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 382030290.0 7490790.0 GSM8784928 r2 0:51 A:100050525;C:89650775;G:91497813;T:100795370;N:35807 51       100050525 89650775 91497813 100795370 35807 SRX27626961 SRS24034228 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34835 34835 SRR32289957 SRX27626960 SRS24034231 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 6dpi biological replicate 2 GSM8784927   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 6dpi biological replicate 2 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784927 GSM8784927: FAC sorted RGCs at 6dpi biological replicate 2; Danio rerio; RNA Seq GSM8784927 r1 GSM8784927 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121311.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 359457486.0 7048186.0 GSM8784927 r1 0:51 A:94049871;C:84581283;G:86196196;T:94595815;N:34321 51       94049871 84581283 86196196 94595815 34321 SRX27626960 SRS24034231 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34836 34836 SRR32289958 SRX27626960 SRS24034231 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 6dpi biological replicate 2 GSM8784927   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 6dpi biological replicate 2 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784927 GSM8784927: FAC sorted RGCs at 6dpi biological replicate 2; Danio rerio; RNA Seq GSM8784927 r1 GSM8784927 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121311.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 368062155.0 7216905.0 GSM8784927 r2 0:51 A:96303888;C:86587511;G:88207050;T:96929121;N:34585 51       96303888 86587511 88207050 96929121 34585 SRX27626960 SRS24034231 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34837 34837 SRR32289959 SRX27626959 SRS24034229 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 6dpi biological replicate 1 GSM8784926   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 6dpi biological replicate 1 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784926 GSM8784926: FAC sorted RGCs at 6dpi biological replicate 1; Danio rerio; RNA Seq GSM8784926 r1 GSM8784926 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121310.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 308100945.0 6041195.0 GSM8784926 r1 0:51 A:86887196;C:64730880;G:65880791;T:90571586;N:30492 51       86887196 64730880 65880791 90571586 30492 SRX27626959 SRS24034229 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34838 34838 SRR32289960 SRX27626959 SRS24034229 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 6dpi biological replicate 1 GSM8784926   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 6dpi biological replicate 1 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784926 GSM8784926: FAC sorted RGCs at 6dpi biological replicate 1; Danio rerio; RNA Seq GSM8784926 r1 GSM8784926 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121310.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 318837465.0 6251715.0 GSM8784926 r2 0:51 A:89949594;C:66936819;G:68101167;T:93818871;N:31014 51       89949594 66936819 68101167 93818871 31014 SRX27626959 SRS24034229 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34839 34839 SRR32289961 SRX27626958 SRS24034226 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 3dpi biological replicate 6 GSM8784925   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 3dpi biological replicate 6 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784925 GSM8784925: FAC sorted RGCs at 3dpi biological replicate 6; Danio rerio; RNA Seq GSM8784925 r1 GSM8784925 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122372.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 330289260.0 6476260.0 GSM8784925 r1 0:51 A:86654778;C:77586975;G:79218167;T:86799619;N:29721 51       86654778 77586975 79218167 86799619 29721 SRX27626958 SRS24034226 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34840 34840 SRR32289962 SRX27626958 SRS24034226 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 3dpi biological replicate 6 GSM8784925   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 3dpi biological replicate 6 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784925 GSM8784925: FAC sorted RGCs at 3dpi biological replicate 6; Danio rerio; RNA Seq GSM8784925 r1 GSM8784925 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122372.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 337840524.0 6624324.0 GSM8784925 r2 0:51 A:88622074;C:79353340;G:80979292;T:88855871;N:29947 51       88622074 79353340 80979292 88855871 29947 SRX27626958 SRS24034226 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34841 34841 SRR32289963 SRX27626957 SRS24034227 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 3dpi biological replicate 5 GSM8784924   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 3dpi biological replicate 5 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784924 GSM8784924: FAC sorted RGCs at 3dpi biological replicate 5; Danio rerio; RNA Seq GSM8784924 r1 GSM8784924 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122371.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 368108820.0 7217820.0 GSM8784924 r1 0:51 A:98464174;C:82788417;G:84631916;T:102188956;N:35357 51       98464174 82788417 84631916 102188956 35357 SRX27626957 SRS24034227 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34842 34842 SRR32289964 SRX27626957 SRS24034227 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 3dpi biological replicate 5 GSM8784924   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 3dpi biological replicate 5 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784924 GSM8784924: FAC sorted RGCs at 3dpi biological replicate 5; Danio rerio; RNA Seq GSM8784924 r1 GSM8784924 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122371.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 378268275.0 7417025.0 GSM8784924 r2 0:51 A:101126361;C:85046503;G:86891002;T:105168387;N:36022 51       101126361 85046503 86891002 105168387 36022 SRX27626957 SRS24034227 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34843 34843 SRR32289965 SRX27626956 SRS24034225 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 3dpi biological replicate 4 GSM8784923   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 3dpi biological replicate 4 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784923 GSM8784923: FAC sorted RGCs at 3dpi biological replicate 4; Danio rerio; RNA Seq GSM8784923 r1 GSM8784923 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121307.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 286509432.0 5617832.0 GSM8784923 r1 0:51 A:73208995;C:69469968;G:70853373;T:72949032;N:28064 51       73208995 69469968 70853373 72949032 28064 SRX27626956 SRS24034225 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34844 34844 SRR32289966 SRX27626956 SRS24034225 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 3dpi biological replicate 4 GSM8784923   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 3dpi biological replicate 4 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784923 GSM8784923: FAC sorted RGCs at 3dpi biological replicate 4; Danio rerio; RNA Seq GSM8784923 r1 GSM8784923 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121307.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 293974863.0 5764213.0 GSM8784923 r2 0:51 A:75131024;C:71285864;G:72635665;T:74893973;N:28337 51       75131024 71285864 72635665 74893973 28337 SRX27626956 SRS24034225 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34845 34845 SRR32289967 SRX27626955 SRS24034223 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 3dpi biological replicate 3 GSM8784922   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 3dpi biological replicate 3 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784922 GSM8784922: FAC sorted RGCs at 3dpi biological replicate 3; Danio rerio; RNA Seq GSM8784922 r1 GSM8784922 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121306.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 358789233.0 7035083.0 GSM8784922 r1 0:51 A:93438522;C:84870850;G:86529862;T:93916370;N:33629 51       93438522 84870850 86529862 93916370 33629 SRX27626955 SRS24034223 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34846 34846 SRR32289968 SRX27626955 SRS24034223 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 3dpi biological replicate 3 GSM8784922   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 3dpi biological replicate 3 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784922 GSM8784922: FAC sorted RGCs at 3dpi biological replicate 3; Danio rerio; RNA Seq GSM8784922 r1 GSM8784922 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121306.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 365025258.0 7157358.0 GSM8784922 r2 0:51 A:95070256;C:86325431;G:87987533;T:95608156;N:33882 51       95070256 86325431 87987533 95608156 33882 SRX27626955 SRS24034223 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34847 34847 SRR32289969 SRX27626954 SRS24034224 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 3dpi biological replicate 2 GSM8784921   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 3dpi biological replicate 2 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784921 GSM8784921: FAC sorted RGCs at 3dpi biological replicate 2; Danio rerio; RNA Seq GSM8784921 r1 GSM8784921 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121305.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 391506702.0 7676602.0 GSM8784921 r1 0:51 A:101960329;C:92790371;G:94697001;T:102022049;N:36952 51       101960329 92790371 94697001 102022049 36952 SRX27626954 SRS24034224 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34848 34848 SRR32289970 SRX27626954 SRS24034224 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 3dpi biological replicate 2 GSM8784921   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 3dpi biological replicate 2 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784921 GSM8784921: FAC sorted RGCs at 3dpi biological replicate 2; Danio rerio; RNA Seq GSM8784921 r1 GSM8784921 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121305.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 401026872.0 7863272.0 GSM8784921 r2 0:51 A:104424027;C:95011852;G:96926223;T:104627136;N:37634 51       104424027 95011852 96926223 104627136 37634 SRX27626954 SRS24034224 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34849 34849 SRR32289971 SRX27626953 SRS24034222 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 3dpi biological replicate 1 GSM8784920   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 3dpi biological replicate 1 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784920 GSM8784920: FAC sorted RGCs at 3dpi biological replicate 1; Danio rerio; RNA Seq GSM8784920 r1 GSM8784920 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121304.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 339021174.0 6647474.0 GSM8784920 r1 0:51 A:93114431;C:74857016;G:76108927;T:94907017;N:33783 51       93114431 74857016 76108927 94907017 33783 SRX27626953 SRS24034222 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34850 34850 SRR32289972 SRX27626953 SRS24034222 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 3dpi biological replicate 1 GSM8784920   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 3dpi biological replicate 1 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784920 GSM8784920: FAC sorted RGCs at 3dpi biological replicate 1; Danio rerio; RNA Seq GSM8784920 r1 GSM8784920 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121304.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 353383896.0 6929096.0 GSM8784920 r2 0:51 A:97070049;C:77993850;G:79259723;T:99025646;N:34628 51       97070049 77993850 79259723 99025646 34628 SRX27626953 SRS24034222 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34851 34851 SRR32289973 SRX27626952 SRS24034220 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 1dpi biological replicate 7 GSM8784919   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 1dpi biological replicate 7 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784919 GSM8784919: FAC sorted RGCs at 1dpi biological replicate 7; Danio rerio; RNA Seq GSM8784919 r1 GSM8784919 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122370.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 394021869.0 7725919.0 GSM8784919 r1 0:51 A:104916639;C:90350948;G:92325077;T:106392449;N:36756 51       104916639 90350948 92325077 106392449 36756 SRX27626952 SRS24034220 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34852 34852 SRR32289974 SRX27626952 SRS24034220 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 1dpi biological replicate 7 GSM8784919   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 1dpi biological replicate 7 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784919 GSM8784919: FAC sorted RGCs at 1dpi biological replicate 7; Danio rerio; RNA Seq GSM8784919 r1 GSM8784919 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122370.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 402835893.0 7898743.0 GSM8784919 r2 0:51 A:107284622;C:92356101;G:94308190;T:108850087;N:36893 51       107284622 92356101 94308190 108850087 36893 SRX27626952 SRS24034220 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34853 34853 SRR32289975 SRX27626951 SRS24034221 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 1dpi biological replicate 6 GSM8784918   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 1dpi biological replicate 6 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784918 GSM8784918: FAC sorted RGCs at 1dpi biological replicate 6; Danio rerio; RNA Seq GSM8784918 r1 GSM8784918 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122368.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 331394226.0 6497926.0 GSM8784918 r1 0:51 A:92193678;C:70679080;G:72151366;T:96339266;N:30836 51       92193678 70679080 72151366 96339266 30836 SRX27626951 SRS24034221 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34854 34854 SRR32289976 SRX27626951 SRS24034221 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 1dpi biological replicate 6 GSM8784918   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 1dpi biological replicate 6 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784918 GSM8784918: FAC sorted RGCs at 1dpi biological replicate 6; Danio rerio; RNA Seq GSM8784918 r1 GSM8784918 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122368.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 341222844.0 6690644.0 GSM8784918 r2 0:51 A:94891966;C:72728396;G:74206983;T:99364490;N:31009 51       94891966 72728396 74206983 99364490 31009 SRX27626951 SRS24034221 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34855 34855 SRR32289977 SRX27626950 SRS24034218 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 1dpi biological replicate 5 GSM8784917   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 1dpi biological replicate 5 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784917 GSM8784917: FAC sorted RGCs at 1dpi biological replicate 5; Danio rerio; RNA Seq GSM8784917 r1 GSM8784917 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122367.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 318762036.0 6250236.0 GSM8784917 r1 0:51 A:88455336;C:66904117;G:68494022;T:94878199;N:30362 51       88455336 66904117 68494022 94878199 30362 SRX27626950 SRS24034218 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34856 34856 SRR32289978 SRX27626950 SRS24034218 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 1dpi biological replicate 5 GSM8784917   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 1dpi biological replicate 5 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784917 GSM8784917: FAC sorted RGCs at 1dpi biological replicate 5; Danio rerio; RNA Seq GSM8784917 r1 GSM8784917 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC122367.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 327003024.0 6411824.0 GSM8784917 r2 0:51 A:90712200;C:68607337;G:70232257;T:97420994;N:30236 51       90712200 68607337 70232257 97420994 30236 SRX27626950 SRS24034218 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34857 34857 SRR32289979 SRX27626949 SRS24034219 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 1dpi biological replicate 4 GSM8784916   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 1dpi biological replicate 4 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784916 GSM8784916: FAC sorted RGCs at 1dpi biological replicate 4; Danio rerio; RNA Seq GSM8784916 r1 GSM8784916 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121301.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 387759885.0 7603135.0 GSM8784916 r1 0:51 A:102783169;C:88945135;G:91353292;T:104641521;N:36768 51       102783169 88945135 91353292 104641521 36768 SRX27626949 SRS24034219 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34858 34858 SRR32289980 SRX27626949 SRS24034219 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 1dpi biological replicate 4 GSM8784916   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 1dpi biological replicate 4 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784916 GSM8784916: FAC sorted RGCs at 1dpi biological replicate 4; Danio rerio; RNA Seq GSM8784916 r1 GSM8784916 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121301.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 397404189.0 7792239.0 GSM8784916 r2 0:51 A:105304214;C:91200661;G:93584392;T:107277465;N:37457 51       105304214 91200661 93584392 107277465 37457 SRX27626949 SRS24034219 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34859 34859 SRR32289981 SRX27626948 SRS24034216 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 1dpi biological replicate 3 GSM8784915   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 1dpi biological replicate 3 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784915 GSM8784915: FAC sorted RGCs at 1dpi biological replicate 3; Danio rerio; RNA Seq GSM8784915 r1 GSM8784915 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121300.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 428248785.0 8397035.0 GSM8784915 r1 0:51 A:112023158;C:100515159;G:102620937;T:113048752;N:40779 51       112023158 100515159 102620937 113048752 40779 SRX27626948 SRS24034216 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34860 34860 SRR32289982 SRX27626948 SRS24034216 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 1dpi biological replicate 3 GSM8784915   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 1dpi biological replicate 3 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784915 GSM8784915: FAC sorted RGCs at 1dpi biological replicate 3; Danio rerio; RNA Seq GSM8784915 r1 GSM8784915 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121300.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 437907063.0 8586413.0 GSM8784915 r2 0:51 A:114573702;C:102734144;G:104841829;T:115716348;N:41040 51       114573702 102734144 104841829 115716348 41040 SRX27626948 SRS24034216 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34861 34861 SRR32289983 SRX27626947 SRS24034217 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 1dpi biological replicate 2 GSM8784914   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 1dpi biological replicate 2 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784914 GSM8784914: FAC sorted RGCs at 1dpi biological replicate 2; Danio rerio; RNA Seq GSM8784914 r1 GSM8784914 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121299.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 402924888.0 7900488.0 GSM8784914 r1 0:51 A:107947778;C:91046861;G:93204506;T:110687203;N:38540 51       107947778 91046861 93204506 110687203 38540 SRX27626947 SRS24034217 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34862 34862 SRR32289984 SRX27626947 SRS24034217 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 1dpi biological replicate 2 GSM8784914   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at 1dpi biological replicate 2 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2 GSM8784914 GSM8784914: FAC sorted RGCs at 1dpi biological replicate 2; Danio rerio; RNA Seq GSM8784914 r1 GSM8784914 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121299.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 413979393.0 8117243.0 GSM8784914 r2 0:51 A:110924319;C:93515017;G:95646686;T:113854113;N:39258 51       110924319 93515017 95646686 113854113 39258 SRX27626947 SRS24034217 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34863 34863 SRR32289985 SRX27626946 SRS24034215 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 1dpi biological replicate 1 GSM8784913   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 1dpi biological replicate 1 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784913 GSM8784913: FAC sorted RGCs at 1dpi biological replicate 1; Danio rerio; RNA Seq GSM8784913 r1 GSM8784913 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121298.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 360875541.0 7075991.0 GSM8784913 r1 0:51 A:102005383;C:74767685;G:76535877;T:107531326;N:35270 51       102005383 74767685 76535877 107531326 35270 SRX27626946 SRS24034215 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34864 34864 SRR32289986 SRX27626946 SRS24034215 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at 1dpi biological replicate 1 GSM8784913   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at 1dpi biological replicate 1 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1 GSM8784913 GSM8784913: FAC sorted RGCs at 1dpi biological replicate 1; Danio rerio; RNA Seq GSM8784913 r1 GSM8784913 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121298.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 372258078.0 7299178.0 GSM8784913 r2 0:51 A:105213098;C:77053267;G:78863209;T:111092762;N:35742 51       105213098 77053267 78863209 111092762 35742 SRX27626946 SRS24034215 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34865 34865 SRR32289987 SRX27626945 SRS24034212 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at naive condition biological replicate 6 GSM8784912   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at naive condition biological replicate 6 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2 GSM8784912 GSM8784912: FAC sorted RGCs at naive condition biological replicate 6; Danio rerio; RNA Seq GSM8784912 r1 GSM8784912 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121295.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 304489992.0 5970392.0 GSM8784912 r1 0:51 A:82425732;C:67909372;G:69611868;T:84514015;N:29005 51       82425732 67909372 69611868 84514015 29005 SRX27626945 SRS24034212 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34866 34866 SRR32289988 SRX27626945 SRS24034212 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at naive condition biological replicate 6 GSM8784912   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at naive condition biological replicate 6 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2 GSM8784912 GSM8784912: FAC sorted RGCs at naive condition biological replicate 6; Danio rerio; RNA Seq GSM8784912 r1 GSM8784912 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121295.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 311693232.0 6111632.0 GSM8784912 r2 0:51 A:84387116;C:69487428;G:71190724;T:86598688;N:29276 51       84387116 69487428 71190724 86598688 29276 SRX27626945 SRS24034212 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34867 34867 SRR32289989 SRX27626944 SRS24034214 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at naive condition biological replicate 5 GSM8784911   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at naive condition biological replicate 5 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2 GSM8784911 GSM8784911: FAC sorted RGCs at naive condition biological replicate 5; Danio rerio; RNA Seq GSM8784911 r1 GSM8784911 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121294.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 371909136.0 7292336.0 GSM8784911 r1 0:51 A:97343920;C:87664048;G:89481936;T:97384353;N:34879 51       97343920 87664048 89481936 97384353 34879 SRX27626944 SRS24034214 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34868 34868 SRR32289990 SRX27626944 SRS24034214 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at naive condition biological replicate 5 GSM8784911   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at naive condition biological replicate 5 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2 GSM8784911 GSM8784911: FAC sorted RGCs at naive condition biological replicate 5; Danio rerio; RNA Seq GSM8784911 r1 GSM8784911 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121294.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 379291284.0 7437084.0 GSM8784911 r2 0:51 A:99243449;C:89397613;G:91207377;T:99407666;N:35179 51       99243449 89397613 91207377 99407666 35179 SRX27626944 SRS24034214 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34869 34869 SRR32289991 SRX27626943 SRS24034213 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at naive condition biological replicate 4 GSM8784910   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at naive condition biological replicate 4 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2 GSM8784910 GSM8784910: FAC sorted RGCs at naive condition biological replicate 4; Danio rerio; RNA Seq GSM8784910 r1 GSM8784910 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121293.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 381808797.0 7486447.0 GSM8784910 r1 0:51 A:102345832;C:86993840;G:89121190;T:103311576;N:36359 51       102345832 86993840 89121190 103311576 36359 SRX27626943 SRS24034213 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34870 34870 SRR32289992 SRX27626943 SRS24034213 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at naive condition biological replicate 4 GSM8784910   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing FAC sorted RGCs at naive condition biological replicate 4 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2 GSM8784910 GSM8784910: FAC sorted RGCs at naive condition biological replicate 4; Danio rerio; RNA Seq GSM8784910 r1 GSM8784910 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121293.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 392824899.0 7702449.0 GSM8784910 r2 0:51 A:105300909;C:89459531;G:91629489;T:106397902;N:37068 51       105300909 89459531 91629489 106397902 37068 SRX27626943 SRS24034213 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34871 34871 SRR32289993 SRX27626942 SRS24034211 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at naive condition biological replicate 3 GSM8784909   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at naive condition biological replicate 3 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 1 GSM8784909 GSM8784909: FAC sorted RGCs at naive condition biological replicate 3; Danio rerio; RNA Seq GSM8784909 r1 GSM8784909 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121292.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 319281267.0 6260417.0 GSM8784909 r1 0:51 A:89536872;C:68243564;G:69702232;T:91767357;N:31242 51       89536872 68243564 69702232 91767357 31242 SRX27626942 SRS24034211 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34872 34872 SRR32289994 SRX27626942 SRS24034211 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at naive condition biological replicate 3 GSM8784909   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at naive condition biological replicate 3 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 1 GSM8784909 GSM8784909: FAC sorted RGCs at naive condition biological replicate 3; Danio rerio; RNA Seq GSM8784909 r1 GSM8784909 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121292.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 330633631.0 6483013.0 GSM8784909 r2 0:51.00 A:92715496;C:70634109;G:72135232;T:95116600;N:32194 51       92715496 70634109 72135232 95116600 32194 SRX27626942 SRS24034211 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34873 34873 SRR32289995 SRX27626941 SRS24034208 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at naive condition biological replicate 2 GSM8784908   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at naive condition biological replicate 2 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 1 GSM8784908 GSM8784908: FAC sorted RGCs at naive condition biological replicate 2; Danio rerio; RNA Seq GSM8784908 r1 GSM8784908 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121291.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 331915752.0 6508152.0 GSM8784908 r1 0:51 A:93895773;C:69919819;G:71545387;T:96523051;N:31722 51       93895773 69919819 71545387 96523051 31722 SRX27626941 SRS24034208 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34874 34874 SRR32289996 SRX27626941 SRS24034208 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at naive condition biological replicate 2 GSM8784908   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at naive condition biological replicate 2 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 1 GSM8784908 GSM8784908: FAC sorted RGCs at naive condition biological replicate 2; Danio rerio; RNA Seq GSM8784908 r1 GSM8784908 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121291.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 341705712.0 6700112.0 GSM8784908 r2 0:51 A:96635678;C:71919743;G:73610334;T:99507718;N:32239 51       96635678 71919743 73610334 99507718 32239 SRX27626941 SRS24034208 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34875 34875 SRR32289997 SRX27626940 SRS24034209 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at naive condition biological replicate 1 GSM8784907   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at naive condition biological replicate 1 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 1 GSM8784907 GSM8784907: FAC sorted RGCs at naive condition biological replicate 1; Danio rerio; RNA Seq GSM8784907 r1 GSM8784907 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121290.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz fastq 373593207.0 7325357.0 GSM8784907 r1 0:51 A:104253639;C:80473294;G:82236043;T:106593718;N:36513 51       104253639 80473294 82236043 106593718 36513 SRX27626940 SRS24034209 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
34876 34876 SRR32289998 SRX27626940 SRS24034209 SRP562853 PRJNA1221797 Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming GSE289140 Transcriptome Analysis Unlike mammals zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously the thioredoxin antioxidant system is upregulated likely to limit oxidative damage. Additionally we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1 3 6 10 and 14 days post optic nerve crush injury.       FAC sorted RGCs at naive condition biological replicate 1 GSM8784907   tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing FAC sorted RGCs at naive condition biological replicate 1 Technical replicates of RNA seq samples were merged post sequencing and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples Retinal ganglion cells   RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer’s instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 1 GSM8784907 GSM8784907: FAC sorted RGCs at naive condition biological replicate 1; Danio rerio; RNA Seq GSM8784907 r1 GSM8784907 1 RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples Nextera XT DNA Illumina San Diego CA USA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP562853     GC121290.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz fastq 384155460.0 7532460.0 GSM8784907 r2 0:51 A:107214095;C:82732789;G:84490928;T:109680699;N:36949 51       107214095 82732789 84490928 109680699 36949 SRX27626940 SRS24034209 SRA2075201 KU Leuven KU Leuven                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2025-02-10 Undetermined Adult Eye Sensory System
41685 41685 SRR5120134 SRX2435377 SRS1870364 SRP095338 PRJNA358049 Transcriptomic Analysis of Adult Zebrafish Inner Ear Hair Cells GSE92559 Transcriptome Analysis To understand the basic biological property of hair cells HCs from lower vertebrates we examined transcriptomes of adult zebrafish HCs. GFP labeled HCs were isolated from the utricle saccule and lagena the three inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. 2 000 HCs and 2 000 non sensory cells from the inner ear were individually collected by suction pipet technique. RNA sequencing was performed and the resulting sequences were mapped analyzed and compared. Comparisons allow us to identify enriched genes in HCs which may underlie HC specialization. Overall design: Examination of transcriptomes of adult zebrafish inner ear hair cells and surrounding cells individually collected and sorted using pou4f3 promoter driven GFP marking hair cells.   pubmed:29406519   GFP neg surrounding cells 1 Technical 2 GSM2432255   tissue:2 000 Inner ear surrounding cells|cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GFP neg surrounding cells 1 Technical 2 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Expression data was exported from CLC Genomics Workbench in the form of Microsoft Excel Spreadsheets. 2 000 Inner ear surrounding cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GSM2432255 GSM2432255: GFP neg surrounding cells 1 Technical 2; Danio rerio; RNA Seq GSM2432255   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2432255 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP095338     fish_WT_CGTACTAG-_L002_R1_001.fastq.gz fastq 2079575456.0 20589856.0 GSM2432255 r1 0:101 A:507789042;C:378574589;G:384399617;T:500198055;N:308614153 101       507789042 378574589 384399617 500198055 308614153 SRX2435377 SRS1870364 SRA505331 GEO Department of Biomedical Sciences, Creighton University 1 0.64962   0.22792   0.76148   0.49037   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2016-12-19 Adult Adult Ear Sensory System
41686 41686 SRR5120133 SRX2435376 SRS1870363 SRP095338 PRJNA358049 Transcriptomic Analysis of Adult Zebrafish Inner Ear Hair Cells GSE92559 Transcriptome Analysis To understand the basic biological property of hair cells HCs from lower vertebrates we examined transcriptomes of adult zebrafish HCs. GFP labeled HCs were isolated from the utricle saccule and lagena the three inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. 2 000 HCs and 2 000 non sensory cells from the inner ear were individually collected by suction pipet technique. RNA sequencing was performed and the resulting sequences were mapped analyzed and compared. Comparisons allow us to identify enriched genes in HCs which may underlie HC specialization. Overall design: Examination of transcriptomes of adult zebrafish inner ear hair cells and surrounding cells individually collected and sorted using pou4f3 promoter driven GFP marking hair cells.   pubmed:29406519   GFP neg surrounding cells 1 Technical 1 GSM2432254   tissue:2 000 Inner ear surrounding cells|cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GFP neg surrounding cells 1 Technical 1 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Expression data was exported from CLC Genomics Workbench in the form of Microsoft Excel Spreadsheets. 2 000 Inner ear surrounding cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GSM2432254 GSM2432254: GFP neg surrounding cells 1 Technical 1; Danio rerio; RNA Seq GSM2432254   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2432254 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP095338     fish_WT_CGTACTAG-_L001_R1_001.fastq.gz fastq 2104552049.0 20837149.0 GSM2432254 r1 0:101 A:514445451;C:383531037;G:389222968;T:506643466;N:310709127 101       514445451 383531037 389222968 506643466 310709127 SRX2435376 SRS1870363 SRA505331 GEO Department of Biomedical Sciences, Creighton University 1 0.6506   0.22936   0.76104   0.48864   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2016-12-19 Adult Adult Ear Sensory System
41687 41687 SRR5120132 SRX2435375 SRS1870362 SRP095338 PRJNA358049 Transcriptomic Analysis of Adult Zebrafish Inner Ear Hair Cells GSE92559 Transcriptome Analysis To understand the basic biological property of hair cells HCs from lower vertebrates we examined transcriptomes of adult zebrafish HCs. GFP labeled HCs were isolated from the utricle saccule and lagena the three inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. 2 000 HCs and 2 000 non sensory cells from the inner ear were individually collected by suction pipet technique. RNA sequencing was performed and the resulting sequences were mapped analyzed and compared. Comparisons allow us to identify enriched genes in HCs which may underlie HC specialization. Overall design: Examination of transcriptomes of adult zebrafish inner ear hair cells and surrounding cells individually collected and sorted using pou4f3 promoter driven GFP marking hair cells.   pubmed:29406519   GFP+ Hair Cells Biological Replicate 2 Technical 2 GSM2432253   tissue:2 000 Inner ear hair cells|cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GFP+ Hair Cells Biological Replicate 2 Technical 2 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Expression data was exported from CLC Genomics Workbench in the form of Microsoft Excel Spreadsheets. 2 000 Inner ear hair cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GSM2432253 GSM2432253: GFP+ Hair Cells Biological Replicate 2 Technical 2; Danio rerio; RNA Seq GSM2432253   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2432253 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP095338     zhc_AGGCAGAA-_L002_R1_001.fastq.gz fastq 6093457260.0 60331260.0 GSM2432253 r1 0:101 A:1471320441;C:1109536878;G:1119505740;T:1436533942;N:956560259 101       1471320441 1109536878 1119505740 1436533942 956560259 SRX2435375 SRS1870362 SRA505331 GEO Department of Biomedical Sciences, Creighton University 1 0.64117   0.14727   0.78145   0.5689   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2016-12-19 Adult Adult Ear Sensory System
41688 41688 SRR5120131 SRX2435374 SRS1870361 SRP095338 PRJNA358049 Transcriptomic Analysis of Adult Zebrafish Inner Ear Hair Cells GSE92559 Transcriptome Analysis To understand the basic biological property of hair cells HCs from lower vertebrates we examined transcriptomes of adult zebrafish HCs. GFP labeled HCs were isolated from the utricle saccule and lagena the three inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. 2 000 HCs and 2 000 non sensory cells from the inner ear were individually collected by suction pipet technique. RNA sequencing was performed and the resulting sequences were mapped analyzed and compared. Comparisons allow us to identify enriched genes in HCs which may underlie HC specialization. Overall design: Examination of transcriptomes of adult zebrafish inner ear hair cells and surrounding cells individually collected and sorted using pou4f3 promoter driven GFP marking hair cells.   pubmed:29406519   GFP+ Hair Cells Biological Replicate 2 Technical 1 GSM2432252   tissue:2 000 Inner ear hair cells|cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GFP+ Hair Cells Biological Replicate 2 Technical 1 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Expression data was exported from CLC Genomics Workbench in the form of Microsoft Excel Spreadsheets. 2 000 Inner ear hair cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GSM2432252 GSM2432252: GFP+ Hair Cells Biological Replicate 2 Technical 1; Danio rerio; RNA Seq GSM2432252   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2432252 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP095338     zhc_AGGCAGAA-_L001_R1_001.fastq.gz fastq 6181180911.0 61199811.0 GSM2432252 r1 0:101 A:1493795643;C:1126661332;G:1135879285;T:1459382790;N:965461861 101       1493795643 1126661332 1135879285 1459382790 965461861 SRX2435374 SRS1870361 SRA505331 GEO Department of Biomedical Sciences, Creighton University 1 0.64372   0.14904   0.78301   0.5671   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2016-12-19 Adult Adult Ear Sensory System
41689 41689 SRR5120130 SRX2435373 SRS1870360 SRP095338 PRJNA358049 Transcriptomic Analysis of Adult Zebrafish Inner Ear Hair Cells GSE92559 Transcriptome Analysis To understand the basic biological property of hair cells HCs from lower vertebrates we examined transcriptomes of adult zebrafish HCs. GFP labeled HCs were isolated from the utricle saccule and lagena the three inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. 2 000 HCs and 2 000 non sensory cells from the inner ear were individually collected by suction pipet technique. RNA sequencing was performed and the resulting sequences were mapped analyzed and compared. Comparisons allow us to identify enriched genes in HCs which may underlie HC specialization. Overall design: Examination of transcriptomes of adult zebrafish inner ear hair cells and surrounding cells individually collected and sorted using pou4f3 promoter driven GFP marking hair cells.   pubmed:29406519   GFP+ Hair Cells Biological Replicate 1 Technical 2 GSM2432251   tissue:2 000 Inner ear hair cells|cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GFP+ Hair Cells Biological Replicate 1 Technical 2 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Expression data was exported from CLC Genomics Workbench in the form of Microsoft Excel Spreadsheets. 2 000 Inner ear hair cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GSM2432251 GSM2432251: GFP+ Hair Cells Biological Replicate 1 Technical 2; Danio rerio; RNA Seq GSM2432251   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2432251 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP095338     fish_TAAGGCGA-_L002_R1_001.fastq.gz fastq 1921914355.0 19028855.0 GSM2432251 r1 0:101 A:477226210;C:364711301;G:374540554;T:470661952;N:234774338 101       477226210 364711301 374540554 470661952 234774338 SRX2435373 SRS1870360 SRA505331 GEO Department of Biomedical Sciences, Creighton University 1 0.68061   0.1576   0.7693   0.59569   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2016-12-19 Adult Adult Ear Sensory System
41690 41690 SRR5120129 SRX2435372 SRS1870359 SRP095338 PRJNA358049 Transcriptomic Analysis of Adult Zebrafish Inner Ear Hair Cells GSE92559 Transcriptome Analysis To understand the basic biological property of hair cells HCs from lower vertebrates we examined transcriptomes of adult zebrafish HCs. GFP labeled HCs were isolated from the utricle saccule and lagena the three inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. 2 000 HCs and 2 000 non sensory cells from the inner ear were individually collected by suction pipet technique. RNA sequencing was performed and the resulting sequences were mapped analyzed and compared. Comparisons allow us to identify enriched genes in HCs which may underlie HC specialization. Overall design: Examination of transcriptomes of adult zebrafish inner ear hair cells and surrounding cells individually collected and sorted using pou4f3 promoter driven GFP marking hair cells.   pubmed:29406519   GFP+ Hair Cells Biological Replicate 1 Technical 1 GSM2432250   tissue:2 000 Inner ear hair cells|cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GFP+ Hair Cells Biological Replicate 1 Technical 1 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Expression data was exported from CLC Genomics Workbench in the form of Microsoft Excel Spreadsheets. 2 000 Inner ear hair cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GSM2432250 GSM2432250: GFP+ Hair Cells Biological Replicate 1 Technical 1; Danio rerio; RNA Seq GSM2432250   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2432250 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP095338     fish_TAAGGCGA-_L001_R1_001.fastq.gz fastq 1946906300.0 19276300.0 GSM2432250 r1 0:101 A:483944927;C:369830453;G:379601203;T:477313685;N:236216032 101       483944927 369830453 379601203 477313685 236216032 SRX2435372 SRS1870359 SRA505331 GEO Department of Biomedical Sciences, Creighton University 1 0.68178   0.1597   0.77019   0.59655   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2016-12-19 Adult Adult Ear Sensory System
42948 42948 SRR5853089 SRX3022436 SRS2371721 SRP113243 PRJNA395227 RNA sequencing of Adult Zebrafish Inner Ear Hair Cells GSE101693 Transcriptome Analysis To understand the basic biological properties of inner ear hair cells HCs from non mammalian vertebrates we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP labeled HCs were isolated from inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. One thousand HCs and 1 000 non sensory surrounding cells nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology function and pathology of adult zebrafish HCs. It also establishes a framework for future characterization of the genes expressed in HCs and for the study of HC evolution. Overall design: One thousand HCs and 1 000 nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization.   pubmed:29406519   GFP neg Control surrounding cells 3 GSM2712284   tissue:1 000 Inner ear surrounding cells|cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GFP neg Control surrounding cells 3 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Excel file of expression data of hair cells and surrounding control cells using RPKM values 1 000 Inner ear surrounding cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GSM2712284 GSM2712284: GFP neg Control surrounding cells 3; Danio rerio; RNA Seq GSM2712284   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2712284 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP113243     ZFControl3_S3_L001_R1_001.fastq.gz ZFControl3_S3_L001_R2_001.fastq.gz fastq fastq 4109673117.0 45498619.0 GSM2712284 r1 0:90.33 1:0 A:1180209080;C:857937316;G:867108081;T:1202304007;N:2114633 90 0     1180209080 857937316 867108081 1202304007 2114633 SRX3022436 SRS2371721 SRA589592 GEO Department of Biomedical Sciences, Creighton University 1 0.89781   0.12518   0.74966   0.65157   40   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2017-07-20 Adult Adult Ear Sensory System
42949 42949 SRR5853087 SRX3022435 SRS2371720 SRP113243 PRJNA395227 RNA sequencing of Adult Zebrafish Inner Ear Hair Cells GSE101693 Transcriptome Analysis To understand the basic biological properties of inner ear hair cells HCs from non mammalian vertebrates we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP labeled HCs were isolated from inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. One thousand HCs and 1 000 non sensory surrounding cells nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology function and pathology of adult zebrafish HCs. It also establishes a framework for future characterization of the genes expressed in HCs and for the study of HC evolution. Overall design: One thousand HCs and 1 000 nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization.   pubmed:29406519   GFP neg Control surrounding cells 2 GSM2712283   tissue:1 000 Inner ear surrounding cells|cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GFP neg Control surrounding cells 2 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Excel file of expression data of hair cells and surrounding control cells using RPKM values 1 000 Inner ear surrounding cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GSM2712283 GSM2712283: GFP neg Control surrounding cells 2; Danio rerio; RNA Seq GSM2712283   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2712283 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP113243     ZFControl2_S2_L001_R1_001.fastq.gz ZFControl2_S2_L001_R2_001.fastq.gz fastq fastq 5277482903.0 59741039.0 GSM2712283 r1 0:88.34 1:0 A:1487835111;C:1133268730;G:1145158631;T:1508220719;N:2999712 88 0     1487835111 1133268730 1145158631 1508220719 2999712 SRX3022435 SRS2371720 SRA589592 GEO Department of Biomedical Sciences, Creighton University 1 0.89608   0.11913   0.74452   0.64488   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2017-07-20 Adult Adult Ear Sensory System
42950 42950 SRR5853085 SRX3022434 SRS2371718 SRP113243 PRJNA395227 RNA sequencing of Adult Zebrafish Inner Ear Hair Cells GSE101693 Transcriptome Analysis To understand the basic biological properties of inner ear hair cells HCs from non mammalian vertebrates we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP labeled HCs were isolated from inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. One thousand HCs and 1 000 non sensory surrounding cells nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology function and pathology of adult zebrafish HCs. It also establishes a framework for future characterization of the genes expressed in HCs and for the study of HC evolution. Overall design: One thousand HCs and 1 000 nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization.   pubmed:29406519   GFP neg Control surrounding cells 1 GSM2712282   tissue:1 000 Inner ear surrounding cells|cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GFP neg Control surrounding cells 1 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Excel file of expression data of hair cells and surrounding control cells using RPKM values 1 000 Inner ear surrounding cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GSM2712282 GSM2712282: GFP neg Control surrounding cells 1; Danio rerio; RNA Seq GSM2712282   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2712282 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP113243     ZFControl1_S1_L001_R1_001.fastq.gz ZFControl1_S1_L001_R2_001.fastq.gz fastq fastq 4884084264.0 54844980.0 GSM2712282 r1 0:89.05 1:0 A:1416754694;C:1002154600;G:1012874728;T:1449240729;N:3059513 89 0     1416754694 1002154600 1012874728 1449240729 3059513 SRX3022434 SRS2371718 SRA589592 GEO Department of Biomedical Sciences, Creighton University 1 0.89495   0.12873   0.74961   0.65345   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2017-07-20 Adult Adult Ear Sensory System
42951 42951 SRR5853084 SRX3022433 SRS2371719 SRP113243 PRJNA395227 RNA sequencing of Adult Zebrafish Inner Ear Hair Cells GSE101693 Transcriptome Analysis To understand the basic biological properties of inner ear hair cells HCs from non mammalian vertebrates we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP labeled HCs were isolated from inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. One thousand HCs and 1 000 non sensory surrounding cells nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology function and pathology of adult zebrafish HCs. It also establishes a framework for future characterization of the genes expressed in HCs and for the study of HC evolution. Overall design: One thousand HCs and 1 000 nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization.   pubmed:29406519   GFP+ Zebrafish Hair Cells Biological Replicate 3 GSM2712281   tissue:1 000 Inner ear hair cells|cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GFP+ Zebrafish Hair Cells Biological Replicate 3 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Excel file of expression data of hair cells and surrounding control cells using RPKM values 1 000 Inner ear hair cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GSM2712281 GSM2712281: GFP+ Zebrafish Hair Cells Biological Replicate 3; Danio rerio; RNA Seq GSM2712281   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2712281 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP113243     ZFgfp+3_S6_L001_R2_001.fastq.gz ZFgfp+3_S6_L001_R1_001.fastq.gz fastq fastq 4519238829.0 50912071.0 GSM2712281 r1 0:88.77 1:0 A:1293161930;C:955006076;G:967428880;T:1300944329;N:2697614 88 0     1293161930 955006076 967428880 1300944329 2697614 SRX3022433 SRS2371719 SRA589592 GEO Department of Biomedical Sciences, Creighton University 1 0.92939   0.14631   0.75485   0.53515   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2017-07-20 Adult Adult Ear Sensory System
42952 42952 SRR5853083 SRX3022432 SRS2371717 SRP113243 PRJNA395227 RNA sequencing of Adult Zebrafish Inner Ear Hair Cells GSE101693 Transcriptome Analysis To understand the basic biological properties of inner ear hair cells HCs from non mammalian vertebrates we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP labeled HCs were isolated from inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. One thousand HCs and 1 000 non sensory surrounding cells nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology function and pathology of adult zebrafish HCs. It also establishes a framework for future characterization of the genes expressed in HCs and for the study of HC evolution. Overall design: One thousand HCs and 1 000 nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization.   pubmed:29406519   GFP+ Zebrafish Hair Cells Biological Replicate 2 GSM2712280   tissue:1 000 Inner ear hair cells|cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GFP+ Zebrafish Hair Cells Biological Replicate 2 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Excel file of expression data of hair cells and surrounding control cells using RPKM values 1 000 Inner ear hair cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GSM2712280 GSM2712280: GFP+ Zebrafish Hair Cells Biological Replicate 2; Danio rerio; RNA Seq GSM2712280   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2712280 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP113243     ZFgfp+2_S5_L001_R1_001.fastq.gz ZFgfp+2_S5_L001_R2_001.fastq.gz fastq fastq 9048065761.0 100567605.0 GSM2712280 r1 0:89.97 1:0 A:2534571144;C:1972906517;G:2001215942;T:2534611481;N:4760677 89 0     2534571144 1972906517 2001215942 2534611481 4760677 SRX3022432 SRS2371717 SRA589592 GEO Department of Biomedical Sciences, Creighton University 1 0.93842   0.12913   0.75402   0.53067   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2017-07-20 Adult Adult Ear Sensory System
42953 42953 SRR5853082 SRX3022431 SRS2371716 SRP113243 PRJNA395227 RNA sequencing of Adult Zebrafish Inner Ear Hair Cells GSE101693 Transcriptome Analysis To understand the basic biological properties of inner ear hair cells HCs from non mammalian vertebrates we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP labeled HCs were isolated from inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. One thousand HCs and 1 000 non sensory surrounding cells nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology function and pathology of adult zebrafish HCs. It also establishes a framework for future characterization of the genes expressed in HCs and for the study of HC evolution. Overall design: One thousand HCs and 1 000 nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization.   pubmed:29406519   GFP+ Zebrafish Hair Cells Biological Replicate 1 GSM2712279   tissue:1 000 Inner ear hair cells|cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GFP+ Zebrafish Hair Cells Biological Replicate 1 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Excel file of expression data of hair cells and surrounding control cells using RPKM values 1 000 Inner ear hair cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GSM2712279 GSM2712279: GFP+ Zebrafish Hair Cells Biological Replicate 1; Danio rerio; RNA Seq GSM2712279   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2712279 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP113243     ZFgfp+1_S4_L001_R1_001.fastq.gz ZFgfp+1_S4_L001_R2_001.fastq.gz fastq fastq 1315401262.0 14413064.0 GSM2712279 r1 0:91.26 1:0 A:370914131;C:284206703;G:289196987;T:370556334;N:527107 91 0     370914131 284206703 289196987 370556334 527107 SRX3022431 SRS2371716 SRA589592 GEO Department of Biomedical Sciences, Creighton University 1 0.93705   0.13551   0.75471   0.53888   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2017-07-20 Adult Adult Ear Sensory System
52368 52368 SRR9189640 SRX5961786 SRS4871024 SRP200281 PRJNA546018 TGFß signaling in retinal tissue repair [Danio Rerio] GSE132141 Transcriptome Analysis In mammals retinal damage is followed by Müller glia cell activation and proliferation. While retinal gliosis persists in adult mammals post an insult or disease some vertebrates including zebrafish have the capacity to regenerate. We believe we are the first group to show that gliosis is a fibrotic like process in mammals' eyes caused by differential activation of canonical and non canonical TGFß signaling pathways. Overall design: Comparison of murine and fish Müller cell transcriptome post retinal injury parent bioproject:PRJNA546014 pubmed:34593012   MC Zf neg 3 GSM3847462   source name:MC Zf neg|strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|tissue:retina|cell type:Muller cells MC Zf neg 3 The raw reads were first cleaned by removing adapter sequences trimming low quality ends and filtering reads with low quality phred quality <20 using Trimmomatic Version 0.36 18. The read alignment was done with STAR v2.6.0c 19. As reference we used the Ensembl zebrafish genome build GRCz10 from 2017 06 07 release 89 and respectively the Ensembl mouse genome build GRCm38.p5 with the gene annotations downloaded on 2018 02 26 from Ensembl release 91. The STAR alignment options were " outFilterType BySJout outFilterMatchNmin 30 outFilterMismatchNmax 10 outFilterMismatchNoverLmax 0.05 alignSJDBoverhangMin 1 alignSJoverhangMin 8 alignIntronMax 1000000 alignMatesGapMax 1000000 outFilterMultimapNmax 50". Gene expression values were computed with the function featureCounts from the R package Rsubread v1.26.0 20. The options for featureCounts were: min mapping quality 10 min feature overlap 10bp count multi mapping reads count only primary alignments count reads also if they overlap multiple genes. To detect differentially expressed genes we applied a count based negative binomial model implemented in the software package DESeq2 R version: 3.5.0 DESeq2 version: 1.20.0. The differential expression was assessed using an exact test adapted for over dispersed data. Genes showing altered expression with an adjusted p value < 0.05 Benjamini and Hochberg method were considered differentially expressed. Genome build: zebrafish genome build GRCz10 Supplementary files format and content: text files holding gread counts per gene MC Zf neg For the zebrafish post anesthesia with 0.16 mg/mL ethyl 3 aminobenzoate methanesulfonate salt Tricaine; Sigma Aldrich Buchs Switzerland dissolved in the tank water 1 2 drops of 2% hydroxypropyl methylcellulose Methocel OmniVision AG Neuhausen Switzerland were topically applied to the cornea. A diode laser with a wavelength of 532 nm Visulas 532s Carl Zeiss Meditec AG Oberkochen Germany was used to create retinal lesions at the region of the posterior pole around the optic nerve 6. These were confined to the ONL and surrounded by apparently healthy retinal tissue. Four laser burns were applied to the left eye: two superior and two inferior to the optic nerve separated from the nerve by at least two lesion diameters. For the RNAseq analysis 20 laser burns were created in both eyes. Each burn was produced with 70 mW of power for 100 ms and aimed to have a diameter of 50 µm 6. The right eye was used as internal negative control. To focus the laser aiming beam on the retina a 2.0 mm laser lens was employed Ocular Instruments Bellevue WA USA. post laser treatment fish were revived by placing them in a container with fresh tank water and creating a water flow over the gills. At different time xxx post injury induction Day 1 3 and 7 both retinas of three gfap:gfap GFP zebrafish per time point were dissected and kept in cold diethyl pyrocarbonate phosphate buffered saline DEPC PBS 12. Enzymatically dissociation was initiated by 0.05% trypsin ThermoFisher Scientific diluted in DEPC PBS at 37 °C for 10 min. Cell suspension was then mechanically triturated trypsin inhibitor 10 mg/ml; Sigma Aldrich added and the solution centrifuged at 1200 rpm for 5 min. Dissociated retinas were resuspended in DEPC PBS with 10% FBS and DNase I 200 U/ml; Roche filtered and collected in Falcon® Round Bottom Tubes with CellStrainer Cap 12x75 mm; Costar Corning Cambridge MA. Hoechst 33342 Ready Flow™ Reagent ThermoFisher Scientific was added as a DNA dye for cell cycle analysis. Cells from gfap:gfap GFP negative siblings were used to determine background fluorescence levels. 100 cells/μl above this threshold were collected from gfap:gfap GFP positive fish using FACS into separate 96 well plates containing 4 μl lysis buffer comprised of Buffer TCL 1031576; Qiagen plus 1% 2 mercaptoethanol 63689; Sigma Aldrich. post cell sorting all samples were immediately frozen at −70°C. Sorted cells were processed using the published Smart seq2 protocol 17 to generate the cDNA libraries. The quality of the RNA cDNA and final libraries was determined using an Agilent 4200 TapeStation System Agilent Santa Clara CA USA. The libraries were pooled and sequenced in an Illumina HiSeq2500 Illumina San Diego CA USA with a depth of around 20 Mio reads per sample.   strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|tissue:retina|cell type:Muller cells GSM3847462 GSM3847462: MC Zf neg 3; Danio rerio; RNA Seq GSM3847462   1 At different time xxx post injury induction Day 1 3 and 7 both retinas of three gfap:gfap GFP zebrafish per time point were dissected and kept in cold diethyl pyrocarbonate phosphate buffered saline DEPC PBS 12. Enzymatically dissociation was initiated by 0.05% trypsin ThermoFisher Scientific diluted in DEPC PBS at 37 °C for 10 min. Cell suspension was then mechanically triturated trypsin inhibitor 10 mg/ml; Sigma Aldrich added and the solution centrifuged at 1200 rpm for 5 min. Dissociated retinas were resuspended in DEPC PBS with 10% FBS and DNase I 200 U/ml; Roche filtered and collected in Falcon® Round Bottom Tubes with CellStrainer Cap 12x75 mm; Costar Corning Cambridge MA. Hoechst 33342 Ready Flow™ Reagent ThermoFisher Scientific was added as a DNA dye for cell cycle analysis. Cells from gfap:gfap GFP negative siblings were used to determine background fluorescence levels. 100 cells/μl above this threshold were collected from gfap:gfap GFP positive fish using FACS into separate 96 well plates containing 4 μl lysis buffer comprised of Buffer TCL 1031576; Qiagen plus 1% 2 mercaptoethanol 63689; Sigma Aldrich. post cell sorting all samples were immediately frozen at −70°C. Sorted cells were processed using the published Smart seq2 protocol 17 to generate the cDNA libraries. The quality of the RNA cDNA and final libraries was determined using an Agilent 4200 TapeStation System Agilent Santa Clara CA USA. The libraries were pooled and sequenced in an Illumina HiSeq2500 Illumina San Diego CA USA with a depth of around 20 Mio reads per sample. GEO Accession:GSM3847462 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP200281     20180726.A-MC__Zf_neg_3_R1.fastq.gz fastq 1615959198.0 12825073.0 GSM3847462 r1 0:126 1:0 A:418533529;C:364287983;G:345223370;T:487814394;N:99922 126 0     418533529 364287983 345223370 487814394 99922 SRX5961786 SRS4871024 SRA893729 GEO Inselspital-University of Bern 1 0.85245   0.27536   0.87507   0.59533   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Switzerland 2019-06-03 Adult Adult Eye Sensory System
52369 52369 SRR9189639 SRX5961785 SRS4871023 SRP200281 PRJNA546018 TGFß signaling in retinal tissue repair [Danio Rerio] GSE132141 Transcriptome Analysis In mammals retinal damage is followed by Müller glia cell activation and proliferation. While retinal gliosis persists in adult mammals post an insult or disease some vertebrates including zebrafish have the capacity to regenerate. We believe we are the first group to show that gliosis is a fibrotic like process in mammals' eyes caused by differential activation of canonical and non canonical TGFß signaling pathways. Overall design: Comparison of murine and fish Müller cell transcriptome post retinal injury parent bioproject:PRJNA546014 pubmed:34593012   MC Zf neg 2 GSM3847461   source name:MC Zf neg|strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|tissue:retina|cell type:Muller cells MC Zf neg 2 The raw reads were first cleaned by removing adapter sequences trimming low quality ends and filtering reads with low quality phred quality <20 using Trimmomatic Version 0.36 18. The read alignment was done with STAR v2.6.0c 19. As reference we used the Ensembl zebrafish genome build GRCz10 from 2017 06 07 release 89 and respectively the Ensembl mouse genome build GRCm38.p5 with the gene annotations downloaded on 2018 02 26 from Ensembl release 91. The STAR alignment options were " outFilterType BySJout outFilterMatchNmin 30 outFilterMismatchNmax 10 outFilterMismatchNoverLmax 0.05 alignSJDBoverhangMin 1 alignSJoverhangMin 8 alignIntronMax 1000000 alignMatesGapMax 1000000 outFilterMultimapNmax 50". Gene expression values were computed with the function featureCounts from the R package Rsubread v1.26.0 20. The options for featureCounts were: min mapping quality 10 min feature overlap 10bp count multi mapping reads count only primary alignments count reads also if they overlap multiple genes. To detect differentially expressed genes we applied a count based negative binomial model implemented in the software package DESeq2 R version: 3.5.0 DESeq2 version: 1.20.0. The differential expression was assessed using an exact test adapted for over dispersed data. Genes showing altered expression with an adjusted p value < 0.05 Benjamini and Hochberg method were considered differentially expressed. Genome build: zebrafish genome build GRCz10 Supplementary files format and content: text files holding gread counts per gene MC Zf neg For the zebrafish post anesthesia with 0.16 mg/mL ethyl 3 aminobenzoate methanesulfonate salt Tricaine; Sigma Aldrich Buchs Switzerland dissolved in the tank water 1 2 drops of 2% hydroxypropyl methylcellulose Methocel OmniVision AG Neuhausen Switzerland were topically applied to the cornea. A diode laser with a wavelength of 532 nm Visulas 532s Carl Zeiss Meditec AG Oberkochen Germany was used to create retinal lesions at the region of the posterior pole around the optic nerve 6. These were confined to the ONL and surrounded by apparently healthy retinal tissue. Four laser burns were applied to the left eye: two superior and two inferior to the optic nerve separated from the nerve by at least two lesion diameters. For the RNAseq analysis 20 laser burns were created in both eyes. Each burn was produced with 70 mW of power for 100 ms and aimed to have a diameter of 50 µm 6. The right eye was used as internal negative control. To focus the laser aiming beam on the retina a 2.0 mm laser lens was employed Ocular Instruments Bellevue WA USA. post laser treatment fish were revived by placing them in a container with fresh tank water and creating a water flow over the gills. At different time xxx post injury induction Day 1 3 and 7 both retinas of three gfap:gfap GFP zebrafish per time point were dissected and kept in cold diethyl pyrocarbonate phosphate buffered saline DEPC PBS 12. Enzymatically dissociation was initiated by 0.05% trypsin ThermoFisher Scientific diluted in DEPC PBS at 37 °C for 10 min. Cell suspension was then mechanically triturated trypsin inhibitor 10 mg/ml; Sigma Aldrich added and the solution centrifuged at 1200 rpm for 5 min. Dissociated retinas were resuspended in DEPC PBS with 10% FBS and DNase I 200 U/ml; Roche filtered and collected in Falcon® Round Bottom Tubes with CellStrainer Cap 12x75 mm; Costar Corning Cambridge MA. Hoechst 33342 Ready Flow™ Reagent ThermoFisher Scientific was added as a DNA dye for cell cycle analysis. Cells from gfap:gfap GFP negative siblings were used to determine background fluorescence levels. 100 cells/μl above this threshold were collected from gfap:gfap GFP positive fish using FACS into separate 96 well plates containing 4 μl lysis buffer comprised of Buffer TCL 1031576; Qiagen plus 1% 2 mercaptoethanol 63689; Sigma Aldrich. post cell sorting all samples were immediately frozen at −70°C. Sorted cells were processed using the published Smart seq2 protocol 17 to generate the cDNA libraries. The quality of the RNA cDNA and final libraries was determined using an Agilent 4200 TapeStation System Agilent Santa Clara CA USA. The libraries were pooled and sequenced in an Illumina HiSeq2500 Illumina San Diego CA USA with a depth of around 20 Mio reads per sample.   strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|tissue:retina|cell type:Muller cells GSM3847461 GSM3847461: MC Zf neg 2; Danio rerio; RNA Seq GSM3847461   1 At different time xxx post injury induction Day 1 3 and 7 both retinas of three gfap:gfap GFP zebrafish per time point were dissected and kept in cold diethyl pyrocarbonate phosphate buffered saline DEPC PBS 12. Enzymatically dissociation was initiated by 0.05% trypsin ThermoFisher Scientific diluted in DEPC PBS at 37 °C for 10 min. Cell suspension was then mechanically triturated trypsin inhibitor 10 mg/ml; Sigma Aldrich added and the solution centrifuged at 1200 rpm for 5 min. Dissociated retinas were resuspended in DEPC PBS with 10% FBS and DNase I 200 U/ml; Roche filtered and collected in Falcon® Round Bottom Tubes with CellStrainer Cap 12x75 mm; Costar Corning Cambridge MA. Hoechst 33342 Ready Flow™ Reagent ThermoFisher Scientific was added as a DNA dye for cell cycle analysis. Cells from gfap:gfap GFP negative siblings were used to determine background fluorescence levels. 100 cells/μl above this threshold were collected from gfap:gfap GFP positive fish using FACS into separate 96 well plates containing 4 μl lysis buffer comprised of Buffer TCL 1031576; Qiagen plus 1% 2 mercaptoethanol 63689; Sigma Aldrich. post cell sorting all samples were immediately frozen at −70°C. Sorted cells were processed using the published Smart seq2 protocol 17 to generate the cDNA libraries. The quality of the RNA cDNA and final libraries was determined using an Agilent 4200 TapeStation System Agilent Santa Clara CA USA. The libraries were pooled and sequenced in an Illumina HiSeq2500 Illumina San Diego CA USA with a depth of around 20 Mio reads per sample. GEO Accession:GSM3847461 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP200281     20180726.A-MC__Zf_neg_2_R1.fastq.gz fastq 2459357838.0 19518713.0 GSM3847461 r1 0:126 1:0 A:624885742;C:553693915;G:517768460;T:762857681;N:152040 126 0     624885742 553693915 517768460 762857681 152040 SRX5961785 SRS4871023 SRA893729 GEO Inselspital-University of Bern 1 0.8151   0.31449   0.86354   0.86096   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Switzerland 2019-06-03 Adult Adult Eye Sensory System
52370 52370 SRR9189638 SRX5961784 SRS4871022 SRP200281 PRJNA546018 TGFß signaling in retinal tissue repair [Danio Rerio] GSE132141 Transcriptome Analysis In mammals retinal damage is followed by Müller glia cell activation and proliferation. While retinal gliosis persists in adult mammals post an insult or disease some vertebrates including zebrafish have the capacity to regenerate. We believe we are the first group to show that gliosis is a fibrotic like process in mammals' eyes caused by differential activation of canonical and non canonical TGFß signaling pathways. Overall design: Comparison of murine and fish Müller cell transcriptome post retinal injury parent bioproject:PRJNA546014 pubmed:34593012   MC Zf neg 1 GSM3847460   source name:MC Zf neg|strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|tissue:retina|cell type:Muller cells MC Zf neg 1 The raw reads were first cleaned by removing adapter sequences trimming low quality ends and filtering reads with low quality phred quality <20 using Trimmomatic Version 0.36 18. The read alignment was done with STAR v2.6.0c 19. As reference we used the Ensembl zebrafish genome build GRCz10 from 2017 06 07 release 89 and respectively the Ensembl mouse genome build GRCm38.p5 with the gene annotations downloaded on 2018 02 26 from Ensembl release 91. The STAR alignment options were " outFilterType BySJout outFilterMatchNmin 30 outFilterMismatchNmax 10 outFilterMismatchNoverLmax 0.05 alignSJDBoverhangMin 1 alignSJoverhangMin 8 alignIntronMax 1000000 alignMatesGapMax 1000000 outFilterMultimapNmax 50". Gene expression values were computed with the function featureCounts from the R package Rsubread v1.26.0 20. The options for featureCounts were: min mapping quality 10 min feature overlap 10bp count multi mapping reads count only primary alignments count reads also if they overlap multiple genes. To detect differentially expressed genes we applied a count based negative binomial model implemented in the software package DESeq2 R version: 3.5.0 DESeq2 version: 1.20.0. The differential expression was assessed using an exact test adapted for over dispersed data. Genes showing altered expression with an adjusted p value < 0.05 Benjamini and Hochberg method were considered differentially expressed. Genome build: zebrafish genome build GRCz10 Supplementary files format and content: text files holding gread counts per gene MC Zf neg For the zebrafish post anesthesia with 0.16 mg/mL ethyl 3 aminobenzoate methanesulfonate salt Tricaine; Sigma Aldrich Buchs Switzerland dissolved in the tank water 1 2 drops of 2% hydroxypropyl methylcellulose Methocel OmniVision AG Neuhausen Switzerland were topically applied to the cornea. A diode laser with a wavelength of 532 nm Visulas 532s Carl Zeiss Meditec AG Oberkochen Germany was used to create retinal lesions at the region of the posterior pole around the optic nerve 6. These were confined to the ONL and surrounded by apparently healthy retinal tissue. Four laser burns were applied to the left eye: two superior and two inferior to the optic nerve separated from the nerve by at least two lesion diameters. For the RNAseq analysis 20 laser burns were created in both eyes. Each burn was produced with 70 mW of power for 100 ms and aimed to have a diameter of 50 µm 6. The right eye was used as internal negative control. To focus the laser aiming beam on the retina a 2.0 mm laser lens was employed Ocular Instruments Bellevue WA USA. post laser treatment fish were revived by placing them in a container with fresh tank water and creating a water flow over the gills. At different time xxx post injury induction Day 1 3 and 7 both retinas of three gfap:gfap GFP zebrafish per time point were dissected and kept in cold diethyl pyrocarbonate phosphate buffered saline DEPC PBS 12. Enzymatically dissociation was initiated by 0.05% trypsin ThermoFisher Scientific diluted in DEPC PBS at 37 °C for 10 min. Cell suspension was then mechanically triturated trypsin inhibitor 10 mg/ml; Sigma Aldrich added and the solution centrifuged at 1200 rpm for 5 min. Dissociated retinas were resuspended in DEPC PBS with 10% FBS and DNase I 200 U/ml; Roche filtered and collected in Falcon® Round Bottom Tubes with CellStrainer Cap 12x75 mm; Costar Corning Cambridge MA. Hoechst 33342 Ready Flow™ Reagent ThermoFisher Scientific was added as a DNA dye for cell cycle analysis. Cells from gfap:gfap GFP negative siblings were used to determine background fluorescence levels. 100 cells/μl above this threshold were collected from gfap:gfap GFP positive fish using FACS into separate 96 well plates containing 4 μl lysis buffer comprised of Buffer TCL 1031576; Qiagen plus 1% 2 mercaptoethanol 63689; Sigma Aldrich. post cell sorting all samples were immediately frozen at −70°C. Sorted cells were processed using the published Smart seq2 protocol 17 to generate the cDNA libraries. The quality of the RNA cDNA and final libraries was determined using an Agilent 4200 TapeStation System Agilent Santa Clara CA USA. The libraries were pooled and sequenced in an Illumina HiSeq2500 Illumina San Diego CA USA with a depth of around 20 Mio reads per sample.   strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|tissue:retina|cell type:Muller cells GSM3847460 GSM3847460: MC Zf neg 1; Danio rerio; RNA Seq GSM3847460   1 At different time xxx post injury induction Day 1 3 and 7 both retinas of three gfap:gfap GFP zebrafish per time point were dissected and kept in cold diethyl pyrocarbonate phosphate buffered saline DEPC PBS 12. Enzymatically dissociation was initiated by 0.05% trypsin ThermoFisher Scientific diluted in DEPC PBS at 37 °C for 10 min. Cell suspension was then mechanically triturated trypsin inhibitor 10 mg/ml; Sigma Aldrich added and the solution centrifuged at 1200 rpm for 5 min. Dissociated retinas were resuspended in DEPC PBS with 10% FBS and DNase I 200 U/ml; Roche filtered and collected in Falcon® Round Bottom Tubes with CellStrainer Cap 12x75 mm; Costar Corning Cambridge MA. Hoechst 33342 Ready Flow™ Reagent ThermoFisher Scientific was added as a DNA dye for cell cycle analysis. Cells from gfap:gfap GFP negative siblings were used to determine background fluorescence levels. 100 cells/μl above this threshold were collected from gfap:gfap GFP positive fish using FACS into separate 96 well plates containing 4 μl lysis buffer comprised of Buffer TCL 1031576; Qiagen plus 1% 2 mercaptoethanol 63689; Sigma Aldrich. post cell sorting all samples were immediately frozen at −70°C. Sorted cells were processed using the published Smart seq2 protocol 17 to generate the cDNA libraries. The quality of the RNA cDNA and final libraries was determined using an Agilent 4200 TapeStation System Agilent Santa Clara CA USA. The libraries were pooled and sequenced in an Illumina HiSeq2500 Illumina San Diego CA USA with a depth of around 20 Mio reads per sample. GEO Accession:GSM3847460 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP200281     20180726.A-MC__Zf_neg_1_R1.fastq.gz fastq 2032355934.0 16129809.0 GSM3847460 r1 0:126 1:0 A:546862586;C:442449456;G:408864931;T:634047443;N:131518 126 0     546862586 442449456 408864931 634047443 131518 SRX5961784 SRS4871022 SRA893729 GEO Inselspital-University of Bern 1 0.76511   0.46783   0.86052   0.82931   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Switzerland 2019-06-03 Adult Adult Eye Sensory System
52371 52371 SRR9189637 SRX5961783 SRS4871021 SRP200281 PRJNA546018 TGFß signaling in retinal tissue repair [Danio Rerio] GSE132141 Transcriptome Analysis In mammals retinal damage is followed by Müller glia cell activation and proliferation. While retinal gliosis persists in adult mammals post an insult or disease some vertebrates including zebrafish have the capacity to regenerate. We believe we are the first group to show that gliosis is a fibrotic like process in mammals' eyes caused by differential activation of canonical and non canonical TGFß signaling pathways. Overall design: Comparison of murine and fish Müller cell transcriptome post retinal injury parent bioproject:PRJNA546014 pubmed:34593012   MC Zf day7 3 GSM3847459   source name:MC Zf day7|strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|time point:7 day post retinal injury|tissue:retina|cell type:Muller cells MC Zf day7 3 The raw reads were first cleaned by removing adapter sequences trimming low quality ends and filtering reads with low quality phred quality <20 using Trimmomatic Version 0.36 18. The read alignment was done with STAR v2.6.0c 19. As reference we used the Ensembl zebrafish genome build GRCz10 from 2017 06 07 release 89 and respectively the Ensembl mouse genome build GRCm38.p5 with the gene annotations downloaded on 2018 02 26 from Ensembl release 91. The STAR alignment options were " outFilterType BySJout outFilterMatchNmin 30 outFilterMismatchNmax 10 outFilterMismatchNoverLmax 0.05 alignSJDBoverhangMin 1 alignSJoverhangMin 8 alignIntronMax 1000000 alignMatesGapMax 1000000 outFilterMultimapNmax 50". Gene expression values were computed with the function featureCounts from the R package Rsubread v1.26.0 20. The options for featureCounts were: min mapping quality 10 min feature overlap 10bp count multi mapping reads count only primary alignments count reads also if they overlap multiple genes. To detect differentially expressed genes we applied a count based negative binomial model implemented in the software package DESeq2 R version: 3.5.0 DESeq2 version: 1.20.0. The differential expression was assessed using an exact test adapted for over dispersed data. Genes showing altered expression with an adjusted p value < 0.05 Benjamini and Hochberg method were considered differentially expressed. Genome build: zebrafish genome build GRCz10 Supplementary files format and content: text files holding gread counts per gene MC Zf day7 For the zebrafish post anesthesia with 0.16 mg/mL ethyl 3 aminobenzoate methanesulfonate salt Tricaine; Sigma Aldrich Buchs Switzerland dissolved in the tank water 1 2 drops of 2% hydroxypropyl methylcellulose Methocel OmniVision AG Neuhausen Switzerland were topically applied to the cornea. A diode laser with a wavelength of 532 nm Visulas 532s Carl Zeiss Meditec AG Oberkochen Germany was used to create retinal lesions at the region of the posterior pole around the optic nerve 6. These were confined to the ONL and surrounded by apparently healthy retinal tissue. Four laser burns were applied to the left eye: two superior and two inferior to the optic nerve separated from the nerve by at least two lesion diameters. For the RNAseq analysis 20 laser burns were created in both eyes. Each burn was produced with 70 mW of power for 100 ms and aimed to have a diameter of 50 µm 6. The right eye was used as internal negative control. To focus the laser aiming beam on the retina a 2.0 mm laser lens was employed Ocular Instruments Bellevue WA USA. post laser treatment fish were revived by placing them in a container with fresh tank water and creating a water flow over the gills. At different time xxx post injury induction Day 1 3 and 7 both retinas of three gfap:gfap GFP zebrafish per time point were dissected and kept in cold diethyl pyrocarbonate phosphate buffered saline DEPC PBS 12. Enzymatically dissociation was initiated by 0.05% trypsin ThermoFisher Scientific diluted in DEPC PBS at 37 °C for 10 min. Cell suspension was then mechanically triturated trypsin inhibitor 10 mg/ml; Sigma Aldrich added and the solution centrifuged at 1200 rpm for 5 min. Dissociated retinas were resuspended in DEPC PBS with 10% FBS and DNase I 200 U/ml; Roche filtered and collected in Falcon® Round Bottom Tubes with CellStrainer Cap 12x75 mm; Costar Corning Cambridge MA. Hoechst 33342 Ready Flow™ Reagent ThermoFisher Scientific was added as a DNA dye for cell cycle analysis. Cells from gfap:gfap GFP negative siblings were used to determine background fluorescence levels. 100 cells/μl above this threshold were collected from gfap:gfap GFP positive fish using FACS into separate 96 well plates containing 4 μl lysis buffer comprised of Buffer TCL 1031576; Qiagen plus 1% 2 mercaptoethanol 63689; Sigma Aldrich. post cell sorting all samples were immediately frozen at −70°C. Sorted cells were processed using the published Smart seq2 protocol 17 to generate the cDNA libraries. The quality of the RNA cDNA and final libraries was determined using an Agilent 4200 TapeStation System Agilent Santa Clara CA USA. The libraries were pooled and sequenced in an Illumina HiSeq2500 Illumina San Diego CA USA with a depth of around 20 Mio reads per sample.   strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|time point:7 day post retinal injury|tissue:retina|cell type:Muller cells GSM3847459 GSM3847459: MC Zf day7 3; Danio rerio; RNA Seq GSM3847459   1 At different time xxx post injury induction Day 1 3 and 7 both retinas of three gfap:gfap GFP zebrafish per time point were dissected and kept in cold diethyl pyrocarbonate phosphate buffered saline DEPC PBS 12. Enzymatically dissociation was initiated by 0.05% trypsin ThermoFisher Scientific diluted in DEPC PBS at 37 °C for 10 min. Cell suspension was then mechanically triturated trypsin inhibitor 10 mg/ml; Sigma Aldrich added and the solution centrifuged at 1200 rpm for 5 min. Dissociated retinas were resuspended in DEPC PBS with 10% FBS and DNase I 200 U/ml; Roche filtered and collected in Falcon® Round Bottom Tubes with CellStrainer Cap 12x75 mm; Costar Corning Cambridge MA. Hoechst 33342 Ready Flow™ Reagent ThermoFisher Scientific was added as a DNA dye for cell cycle analysis. Cells from gfap:gfap GFP negative siblings were used to determine background fluorescence levels. 100 cells/μl above this threshold were collected from gfap:gfap GFP positive fish using FACS into separate 96 well plates containing 4 μl lysis buffer comprised of Buffer TCL 1031576; Qiagen plus 1% 2 mercaptoethanol 63689; Sigma Aldrich. post cell sorting all samples were immediately frozen at −70°C. Sorted cells were processed using the published Smart seq2 protocol 17 to generate the cDNA libraries. The quality of the RNA cDNA and final libraries was determined using an Agilent 4200 TapeStation System Agilent Santa Clara CA USA. The libraries were pooled and sequenced in an Illumina HiSeq2500 Illumina San Diego CA USA with a depth of around 20 Mio reads per sample. GEO Accession:GSM3847459 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP200281     20180726.A-MC__Zf_day7_3_R1.fastq.gz fastq 3436152174.0 27271049.0 GSM3847459 r1 0:126 1:0 A:912581017;C:819539807;G:786606788;T:917236627;N:187935 126 0     912581017 819539807 786606788 917236627 187935 SRX5961783 SRS4871021 SRA893729 GEO Inselspital-University of Bern 1 0.81696   0.2649   0.79579   0.73111   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Switzerland 2019-06-03 Adult Adult Eye Sensory 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");;