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144 rows where experiment.library_selection = "cDNA", technology = "smartseq" and tissue_curation = "Eye"

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devstage_curation_coarse 3

devstage_curation 3

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Eye · 144 ✖

technology 1

  • smartseq · 144 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • cDNA · 144 ✖
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
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
52372 52372 SRR9189636 SRX5961782 SRS4871020 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 2 GSM3847458   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 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 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 GSM3847458 GSM3847458: MC Zf day7 2; Danio rerio; RNA Seq GSM3847458   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:GSM3847458 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP200281     20180726.A-MC__Zf_day7_2_R1.fastq.gz fastq 3124904832.0 24800832.0 GSM3847458 r1 0:126 1:0 A:822659597;C:714047534;G:680615719;T:907389743;N:192239 126 0     822659597 714047534 680615719 907389743 192239 SRX5961782 SRS4871020 SRA893729 GEO Inselspital-University of Bern 1 0.80643   0.36409   0.79403   0.75604   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
52373 52373 SRR9189635 SRX5961781 SRS4871019 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 1 GSM3847457   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 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 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 GSM3847457 GSM3847457: MC Zf day7 1; Danio rerio; RNA Seq GSM3847457   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:GSM3847457 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP200281     20180726.A-MC__Zf_day7_1_R1.fastq.gz fastq 3632720238.0 28831113.0 GSM3847457 r1 0:126 1:0 A:966154990;C:814387800;G:785847147;T:1066118106;N:212195 126 0     966154990 814387800 785847147 1066118106 212195 SRX5961781 SRS4871019 SRA893729 GEO Inselspital-University of Bern 1 0.75217   0.37888   0.81657   0.78911   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
52374 52374 SRR9189634 SRX5961780 SRS4871018 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 day3 3 GSM3847456   source name:MC Zf day3|strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|time point:3 day post retinal injury|tissue:retina|cell type:Muller cells MC Zf day3 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 day3 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:3 day post retinal injury|tissue:retina|cell type:Muller cells GSM3847456 GSM3847456: MC Zf day3 3; Danio rerio; RNA Seq GSM3847456   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:GSM3847456 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP200281     20180726.A-MC__Zf_day3_3_R1.fastq.gz fastq 3430223874.0 27223999.0 GSM3847456 r1 0:126 1:0 A:905801826;C:757490201;G:728052608;T:1038680161;N:199078 126 0     905801826 757490201 728052608 1038680161 199078 SRX5961780 SRS4871018 SRA893729 GEO Inselspital-University of Bern 1 0.8564   0.2565   0.85914   0.87338   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
52375 52375 SRR9189633 SRX5961779 SRS4871017 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 day3 2 GSM3847455   source name:MC Zf day3|strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|time point:3 day post retinal injury|tissue:retina|cell type:Muller cells MC Zf day3 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 day3 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:3 day post retinal injury|tissue:retina|cell type:Muller cells GSM3847455 GSM3847455: MC Zf day3 2; Danio rerio; RNA Seq GSM3847455   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:GSM3847455 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP200281     20180726.A-MC__Zf_day3_2_R1.fastq.gz fastq 3850833420.0 30562170.0 GSM3847455 r1 0:126 1:0 A:1000127340;C:861641422;G:816300090;T:1172533333;N:231235 126 0     1000127340 861641422 816300090 1172533333 231235 SRX5961779 SRS4871017 SRA893729 GEO Inselspital-University of Bern 1 0.85282   0.21844   0.87844   0.85186   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
52376 52376 SRR9189632 SRX5961778 SRS4871016 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 day3 1 GSM3847454   source name:MC Zf day3|strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|time point:3 day post retinal injury|tissue:retina|cell type:Muller cells MC Zf day3 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 day3 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:3 day post retinal injury|tissue:retina|cell type:Muller cells GSM3847454 GSM3847454: MC Zf day3 1; Danio rerio; RNA Seq GSM3847454   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:GSM3847454 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP200281     20180726.A-MC__Zf_day3_1_R1.fastq.gz fastq 5924172492.0 47017242.0 GSM3847454 r1 0:126 1:0 A:1521949708;C:1319818493;G:1255577522;T:1826458571;N:368198 126 0     1521949708 1319818493 1255577522 1826458571 368198 SRX5961778 SRS4871016 SRA893729 GEO Inselspital-University of Bern 1 0.83064   0.29314   0.84867   0.81369   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
52377 52377 SRR9189631 SRX5961777 SRS4871014 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 day1 3 GSM3847453   source name:MC Zf day1|strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|time point:1 day post retinal injury|tissue:retina|cell type:Muller cells MC Zf day1 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 day1 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:1 day post retinal injury|tissue:retina|cell type:Muller cells GSM3847453 GSM3847453: MC Zf day1 3; Danio rerio; RNA Seq GSM3847453   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:GSM3847453 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP200281     20180726.A-MC__Zf_day1_3_R1.fastq.gz fastq 2781271836.0 22073586.0 GSM3847453 r1 0:126 1:0 A:716692348;C:619972643;G:582673456;T:861796308;N:137081 126 0     716692348 619972643 582673456 861796308 137081 SRX5961777 SRS4871014 SRA893729 GEO Inselspital-University of Bern 1 0.78671   0.34442   0.85309   0.78197   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
52378 52378 SRR9189630 SRX5961776 SRS4871015 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 day1 2 GSM3847452   source name:MC Zf day1|strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|time point:1 day post retinal injury|tissue:retina|cell type:Muller cells MC Zf day1 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 day1 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:1 day post retinal injury|tissue:retina|cell type:Muller cells GSM3847452 GSM3847452: MC Zf day1 2; Danio rerio; RNA Seq GSM3847452   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:GSM3847452 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP200281     20180726.A-MC__Zf_day1_2_R1.fastq.gz fastq 2274372702.0 18050577.0 GSM3847452 r1 0:126 1:0 A:613158702;C:487014163;G:470808925;T:703257993;N:132919 126 0     613158702 487014163 470808925 703257993 132919 SRX5961776 SRS4871015 SRA893729 GEO Inselspital-University of Bern 1 0.83234   0.31485   0.85064   0.87684   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
52379 52379 SRR9189629 SRX5961775 SRS4871013 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 day1 1 GSM3847451   source name:MC Zf day1|strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|time point:1 day post retinal injury|tissue:retina|cell type:Muller cells MC Zf day1 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 day1 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:1 day post retinal injury|tissue:retina|cell type:Muller cells GSM3847451 GSM3847451: MC Zf day1 1; Danio rerio; RNA Seq GSM3847451   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:GSM3847451 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP200281     20180726.A-MC__Zf_day1_1_R1.fastq.gz fastq 2080602342.0 16512717.0 GSM3847451 r1 0:126 1:0 A:525963666;C:455898693;G:420126273;T:678474660;N:139050 126 0     525963666 455898693 420126273 678474660 139050 SRX5961775 SRS4871013 SRA893729 GEO Inselspital-University of Bern 1 0.74651   0.31086   0.86529   0.83706   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
60520 60520 SRR12340458 SRX8840229 SRS7103463 SRP273985 PRJNA649260 THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE] GSE155294 Transcriptome Analysis Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.   pubmed:34006636   Gross B1 3 1 18 S6 R1 001 GSM4698653   tissue:retinal pigment epithelium|treatment:MTZ+|time point:7dpi|replicate:3 Gross B1 3 1 18 S6 R1 001 All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint retinal pigment epithelium A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium ≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment. treatment:MTZ+|time point:7dpi|replicate:3 GSM4698653 GSM4698653: Gross B1 3 1 18 S6 R1 001; Danio rerio; RNA Seq GSM4698653   1 ≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions GEO Accession:GSM4698653 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP273985     Gross_B1_3_1_18_S6_R1_001.fastq.gz Gross_B1_3_1_18_S6_R2_001.fastq.gz fastq fastq 8696093700.0 57973958.0 GSM4698653 r1 0:75 1:75 A:2444655785;C:1908991493;G:1829109199;T:2511690358;N:1646865 75 75     2444655785 1908991493 1829109199 2511690358 1646865 SRX8840229 SRS7103463 SRA1104764 GEO Ophthalmology, University of Pittsburgh School Of Medicine 2 0.88587 0.88723 0.15974 0.15917 0.78248 0.78464 0.59661 0.57767 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-07-28 Larval Larval Eye Sensory System
60521 60521 SRR12340457 SRX8840228 SRS7103462 SRP273985 PRJNA649260 THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE] GSE155294 Transcriptome Analysis Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.   pubmed:34006636   Gross A1 3 1 18 S5 R1 001 GSM4698652   tissue:retinal pigment epithelium|treatment:MTZ |time point:7dpi|replicate:3 Gross A1 3 1 18 S5 R1 001 All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint retinal pigment epithelium A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium ≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment. treatment:MTZ |time point:7dpi|replicate:3 GSM4698652 GSM4698652: Gross A1 3 1 18 S5 R1 001; Danio rerio; RNA Seq GSM4698652   1 ≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions GEO Accession:GSM4698652 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP273985     Gross_A1_3_1_18_S5_R1_001.fastq.gz Gross_A1_3_1_18_S5_R2_001.fastq.gz fastq fastq 8604655350.0 57364369.0 GSM4698652 r1 0:75 1:75 A:2438039854;C:1874282641;G:1790105674;T:2500628946;N:1598235 75 75     2438039854 1874282641 1790105674 2500628946 1598235 SRX8840228 SRS7103462 SRA1104764 GEO Ophthalmology, University of Pittsburgh School Of Medicine 2 0.88472 0.88444 0.19788 0.19728 0.79044 0.79403 0.56866 0.56514 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-07-28 Larval Larval Eye Sensory System
60522 60522 SRR12340456 SRX8840227 SRS7103461 SRP273985 PRJNA649260 THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE] GSE155294 Transcriptome Analysis Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.   pubmed:34006636   Gross 4 2 19 18 S8 R1 001 GSM4698651   tissue:retinal pigment epithelium|treatment:MTZ+|time point:7dpi|replicate:2 Gross 4 2 19 18 S8 R1 001 All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint retinal pigment epithelium A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium ≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment. treatment:MTZ+|time point:7dpi|replicate:2 GSM4698651 GSM4698651: Gross 4 2 19 18 S8 R1 001; Danio rerio; RNA Seq GSM4698651   1 ≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions GEO Accession:GSM4698651 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP273985     Gross_4_2_19_18_S8_R1_001.fastq.gz Gross_4_2_19_18_S8_R2_001.fastq.gz fastq fastq 6302384400.0 42015896.0 GSM4698651 r1 0:75 1:75 A:1786664016;C:1362370577;G:1317481284;T:1834695852;N:1172671 75 75     1786664016 1362370577 1317481284 1834695852 1172671 SRX8840227 SRS7103461 SRA1104764 GEO Ophthalmology, University of Pittsburgh School Of Medicine 2 0.8904 0.89048 0.15097 0.15117 0.79957 0.8031 0.60565 0.60374 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-07-28 Larval Larval Eye Sensory System
60523 60523 SRR12340455 SRX8840226 SRS7103460 SRP273985 PRJNA649260 THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE] GSE155294 Transcriptome Analysis Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.   pubmed:34006636   Gross 3 2 19 18 S7 R1 001 GSM4698650   tissue:retinal pigment epithelium|treatment:MTZ |time point:7dpi|replicate:2 Gross 3 2 19 18 S7 R1 001 All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint retinal pigment epithelium A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium ≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment. treatment:MTZ |time point:7dpi|replicate:2 GSM4698650 GSM4698650: Gross 3 2 19 18 S7 R1 001; Danio rerio; RNA Seq GSM4698650   1 ≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions GEO Accession:GSM4698650 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP273985     Gross_3_2_19_18_S7_R1_001.fastq.gz Gross_3_2_19_18_S7_R2_001.fastq.gz fastq fastq 7396105650.0 49307371.0 GSM4698650 r1 0:75 1:75 A:2105808739;C:1588742948;G:1533387574;T:2166793401;N:1372988 75 75     2105808739 1588742948 1533387574 2166793401 1372988 SRX8840226 SRS7103460 SRA1104764 GEO Ophthalmology, University of Pittsburgh School Of Medicine 2 0.88242 0.88279 0.1914 0.19151 0.79366 0.79717 0.59226 0.60319 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-07-28 Larval Larval 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");;