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
29113,SRR27151348,SRX22832950,SRS19813390,SRP476686,PRJNA1050286,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [adult],GSE249754,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,Adult retina  samd7 /   rep3,GSM7963654,,source name:retina|tissue:retina|developmental stage:adult|genotype:samd7 / |geo loc name:missing|collection date:missing,Adult retina  samd7 /   rep3,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from adult retina. Genes are ranked by p adj.,retina,,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:retina|developmental stage:adult|genotype:samd7 / ,GSM7963654,GSM7963654: Adult retina  samd7 /   rep3; Danio rerio; RNA Seq,GSM7963654 r1,GSM7963654,1,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476686,,loader:fastq load.py,samd7 3.GTCGACTCCT-ACCTTAGCCG.HJNJTDSX3_GTCGACTCCT-ACCTTAGCCG_L003_R2.fastq.gz samd7 3.GTCGACTCCT-ACCTTAGCCG.HJNJTDSX3_GTCGACTCCT-ACCTTAGCCG_L003_R1.fastq.gz,fastq fastq,12350621596.0,40896098.0,GSM7963654 r1,0:151 1:151,A:3311452403;C:2805529783;G:3049468848;T:3184114382;N:56180,151,151,,,3311452403,2805529783,3049468848,3184114382,56180,SRX22832950,SRS19813390,SRA1765771,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.9517,0.9527,0.08772,0.08879,0.73342,0.73574,0.50684,0.51229,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Adult,Adult,Eye,Sensory System
29114,SRR27151349,SRX22832949,SRS19813389,SRP476686,PRJNA1050286,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [adult],GSE249754,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,Adult retina  samd7 /   rep2,GSM7963653,,source name:retina|tissue:retina|developmental stage:adult|genotype:samd7 / |geo loc name:missing|collection date:missing,Adult retina  samd7 /   rep2,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from adult retina. Genes are ranked by p adj.,retina,,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:retina|developmental stage:adult|genotype:samd7 / ,GSM7963653,GSM7963653: Adult retina  samd7 /   rep2; Danio rerio; RNA Seq,GSM7963653 r1,GSM7963653,1,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476686,,loader:fastq load.py,samd7 2.AACACCAATG-GCACTTACAA.HJNJTDSX3_AACACCAATG-GCACTTACAA_L003_R2.fastq.gz samd7 2.AACACCAATG-GCACTTACAA.HJNJTDSX3_AACACCAATG-GCACTTACAA_L003_R1.fastq.gz,fastq fastq,10779711820.0,35694410.0,GSM7963653 r1,0:151 1:151,A:2944031330;C:2416631581;G:2607925305;T:2811076060;N:47544,151,151,,,2944031330,2416631581,2607925305,2811076060,47544,SRX22832949,SRS19813389,SRA1765771,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.94587,0.94807,0.0994,0.10023,0.73837,0.74052,0.50262,0.50849,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Adult,Adult,Eye,Sensory System
29115,SRR27151350,SRX22832948,SRS19813387,SRP476686,PRJNA1050286,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [adult],GSE249754,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,Adult retina  samd7 /   rep1,GSM7963652,,source name:retina|tissue:retina|developmental stage:adult|genotype:samd7 / |geo loc name:missing|collection date:missing,Adult retina  samd7 /   rep1,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from adult retina. Genes are ranked by p adj.,retina,,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:retina|developmental stage:adult|genotype:samd7 / ,GSM7963652,GSM7963652: Adult retina  samd7 /   rep1; Danio rerio; RNA Seq,GSM7963652 r1,GSM7963652,1,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476686,,loader:fastq load.py,samd7 1.AGAACTGGTG-TGGATTGTAG.HJNJTDSX3_AGAACTGGTG-TGGATTGTAG_L003_R1.fastq.gz samd7 1.AGAACTGGTG-TGGATTGTAG.HJNJTDSX3_AGAACTGGTG-TGGATTGTAG_L003_R2.fastq.gz,fastq fastq,10592879520.0,35075760.0,GSM7963652 r1,0:151 1:151,A:2902239961;C:2373635807;G:2559549595;T:2757407466;N:46691,151,151,,,2902239961,2373635807,2559549595,2757407466,46691,SRX22832948,SRS19813387,SRA1765771,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.94718,0.94948,0.09134,0.09292,0.7291,0.73117,0.51985,0.52005,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Adult,Adult,Eye,Sensory System
29116,SRR27151351,SRX22832947,SRS19813388,SRP476686,PRJNA1050286,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [adult],GSE249754,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,Adult retina  WT  rep3,GSM7963651,,source name:retina|tissue:retina|developmental stage:adult|genotype:WT|geo loc name:missing|collection date:missing,Adult retina  WT  rep3,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from adult retina. Genes are ranked by p adj.,retina,,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:retina|developmental stage:adult|genotype:WT,GSM7963651,GSM7963651: Adult retina  WT  rep3; Danio rerio; RNA Seq,GSM7963651 r1,GSM7963651,1,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476686,,loader:fastq load.py,wt 3.TCCGAAGTGG-ACACAATGGT.HJNJTDSX3_TCCGAAGTGG-ACACAATGGT_L003_R1.fastq.gz wt 3.TCCGAAGTGG-ACACAATGGT.HJNJTDSX3_TCCGAAGTGG-ACACAATGGT_L003_R2.fastq.gz,fastq fastq,11864600916.0,39286758.0,GSM7963651 r1,0:151 1:151,A:3134961848;C:2656797227;G:3067645293;T:3005143714;N:52834,151,151,,,3134961848,2656797227,3067645293,3005143714,52834,SRX22832947,SRS19813388,SRA1765771,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.94961,0.95129,0.08731,0.08788,0.75465,0.75739,0.52752,0.51933,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Adult,Adult,Eye,Sensory System
29117,SRR27151352,SRX22832946,SRS19813385,SRP476686,PRJNA1050286,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [adult],GSE249754,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,Adult retina  WT  rep2,GSM7963650,,source name:retina|tissue:retina|developmental stage:adult|genotype:WT|geo loc name:missing|collection date:missing,Adult retina  WT  rep2,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from adult retina. Genes are ranked by p adj.,retina,,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:retina|developmental stage:adult|genotype:WT,GSM7963650,GSM7963650: Adult retina  WT  rep2; Danio rerio; RNA Seq,GSM7963650 r1,GSM7963650,1,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476686,,loader:fastq load.py,wt 2.CGATAGCAGG-TAAGTGTCGA.HJNJTDSX3_CGATAGCAGG-TAAGTGTCGA_L003_R1.fastq.gz wt 2.CGATAGCAGG-TAAGTGTCGA.HJNJTDSX3_CGATAGCAGG-TAAGTGTCGA_L003_R2.fastq.gz,fastq fastq,11537286672.0,38202936.0,GSM7963650 r1,0:151 1:151,A:3128579183;C:2619829672;G:2797531802;T:2991294275;N:51740,151,151,,,3128579183,2619829672,2797531802,2991294275,51740,SRX22832946,SRS19813385,SRA1765771,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.95108,0.9523,0.08612,0.08648,0.754,0.75643,0.5265,0.51457,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Adult,Adult,Eye,Sensory System
29118,SRR27151353,SRX22832945,SRS19813386,SRP476686,PRJNA1050286,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [adult],GSE249754,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,Adult retina  WT  rep1,GSM7963649,,source name:retina|tissue:retina|developmental stage:adult|genotype:WT|geo loc name:missing|collection date:missing,Adult retina  WT  rep1,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from adult retina. Genes are ranked by p adj.,retina,,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:retina|developmental stage:adult|genotype:WT,GSM7963649,GSM7963649: Adult retina  WT  rep1; Danio rerio; RNA Seq,GSM7963649 r1,GSM7963649,1,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476686,,loader:fastq load.py,wt 1.AACACCGGTT-ACGAGACGTC.HJNJTDSX3_AACACCGGTT-ACGAGACGTC_L003_R2.fastq.gz wt 1.AACACCGGTT-ACGAGACGTC.HJNJTDSX3_AACACCGGTT-ACGAGACGTC_L003_R1.fastq.gz,fastq fastq,15142192118.0,50139709.0,GSM7963649 r1,0:151 1:151,A:4123269688;C:3413024919;G:3665579705;T:3940250217;N:67589,151,151,,,4123269688,3413024919,3665579705,3940250217,67589,SRX22832945,SRS19813386,SRA1765771,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.94752,0.94913,0.08393,0.08515,0.75446,0.75672,0.46043,0.506,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Adult,Adult,Eye,Sensory System
30230,SRR27730907,SRX23396554,SRS20257429,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,4dpi40Hz+biological replicate 2,,4dpi40Hz 2,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:10|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165700aR1AL1A,M23165700aR1AL1A,4 xxx post injury+40Hz,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,4dpi40Hz_2_1.fq.gz 4dpi40Hz_2_2.fq.gz,fastq fastq,7794055500.0,25980185.0,4dpi40Hz 2 1.fq.gz,0:150 1:150,A:2129184357;C:1759642251;G:1791618685;T:2113568820;N:41387,150,150,,,2129184357,1759642251,1791618685,2113568820,41387,SRX23396554,SRS20257429,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30231,SRR27730908,SRX23396553,SRS20257428,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,4dpi40Hz+biological replicate 1,,4dpi40Hz 1,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:9|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165699aR1AL1A,M23165699aR1AL1A,4 xxx post injury+40Hz,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,4dpi40Hz_1_1.fq.gz 4dpi40Hz_1_2.fq.gz,fastq fastq,7508652600.0,25028842.0,4dpi40Hz 1 1.fq.gz,0:150 1:150,A:2057198043;C:1689714910;G:1722042670;T:2039656491;N:40486,150,150,,,2057198043,1689714910,1722042670,2039656491,40486,SRX23396553,SRS20257428,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30232,SRR27730909,SRX23396552,SRS20257427,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,4dpi+biological replicate 4,,4dpi 4,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:8|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165697aR1AL1A,M23165697aR1AL1A,4 xxx post injury,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,4dpi_4_1.fq.gz 4dpi_4_2.fq.gz,fastq fastq,7094977200.0,23649924.0,4dpi 4 1.fq.gz,0:150 1:150,A:1943019606;C:1597025881;G:1626301543;T:1928592039;N:38131,150,150,,,1943019606,1597025881,1626301543,1928592039,38131,SRX23396552,SRS20257427,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30233,SRR27730910,SRX23396551,SRS20257426,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,4dpi+biological replicate 3,,4dpi 3,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:7|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165696aR1AL1A,M23165696aR1AL1A,4 xxx post injury,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,4dpi_3_1.fq.gz 4dpi_3_2.fq.gz,fastq fastq,7386629700.0,24622099.0,4dpi 3 1.fq.gz,0:150 1:150,A:2031801635;C:1655982922;G:1683647412;T:2015157737;N:39994,150,150,,,2031801635,1655982922,1683647412,2015157737,39994,SRX23396551,SRS20257426,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30234,SRR27730911,SRX23396550,SRS20257425,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,4dpi+biological replicate 2,,4dpi 2,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:6|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165695aR1AL1A,M23165695aR1AL1A,4 xxx post injury,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,4dpi_2_1.fq.gz 4dpi_2_2.fq.gz,fastq fastq,6654237600.0,22180792.0,4dpi 2 1.fq.gz,0:150 1:150,A:1825547718;C:1496727215;G:1522459901;T:1809467151;N:35615,150,150,,,1825547718,1496727215,1522459901,1809467151,35615,SRX23396550,SRS20257425,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30235,SRR27730912,SRX23396549,SRS20257424,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,4dpi+biological replicate 1,,4dpi 1,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:5|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165694aR1AL1A,M23165694aR1AL1A,4 xxx post injury,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,4dpi_1_1.fq.gz 4dpi_1_2.fq.gz,fastq fastq,7023034200.0,23410114.0,4dpi 1 1.fq.gz,0:150 1:150,A:1928523555;C:1581982138;G:1606070304;T:1906420119;N:38084,150,150,,,1928523555,1581982138,1606070304,1906420119,38084,SRX23396549,SRS20257424,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30236,SRR27730913,SRX23396548,SRS20257423,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,Con+biological replicate 4,,Con 4,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:4|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165693aR1AL1A,M23165693aR1AL1A,Control,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,Con_4_1.fq.gz Con_4_2.fq.gz,fastq fastq,6857548800.0,22858496.0,Con 4 1.fq.gz,0:150 1:150,A:1882601360;C:1546021101;G:1569334195;T:1859555495;N:36649,150,150,,,1882601360,1546021101,1569334195,1859555495,36649,SRX23396548,SRS20257423,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30237,SRR27730914,SRX23396547,SRS20257422,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,Con+biological replicate 3,,Con 3,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165692aR1AL1A,M23165692aR1AL1A,Control,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,Con_3_1.fq.gz Con_3_2.fq.gz,fastq fastq,7458957900.0,24863193.0,Con 3 1.fq.gz,0:150 1:150,A:2038911157;C:1679971639;G:1712675120;T:2027359083;N:40901,150,150,,,2038911157,1679971639,1712675120,2027359083,40901,SRX23396547,SRS20257422,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30238,SRR27730915,SRX23396546,SRS20257421,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,7dpi40Hz+biological replicate 4,,7dpi40Hz 4,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:20|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165713aR1AL1A,M23165713aR1AL1A,7 xxx post injury+40Hz,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,7dpi40Hz_4_1.fq.gz 7dpi40Hz_4_2.fq.gz,fastq fastq,6691700400.0,22305668.0,7dpi40Hz 4 1.fq.gz,0:150 1:150,A:1868931421;C:1476540468;G:1501092489;T:1845097964;N:38058,150,150,,,1868931421,1476540468,1501092489,1845097964,38058,SRX23396546,SRS20257421,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30239,SRR27730916,SRX23396545,SRS20257420,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,7dpi40Hz+biological replicate 3,,7dpi40Hz 3,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:19|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165712aR1AL1A,M23165712aR1AL1A,7 xxx post injury+40Hz,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,7dpi40Hz_3_1.fq.gz 7dpi40Hz_3_2.fq.gz,fastq fastq,7212117000.0,24040390.0,7dpi40Hz 3 1.fq.gz,0:150 1:150,A:1992256057;C:1607062903;G:1637554739;T:1975202488;N:40813,150,150,,,1992256057,1607062903,1637554739,1975202488,40813,SRX23396545,SRS20257420,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30240,SRR27730917,SRX23396544,SRS20257419,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,7dpi40Hz+biological replicate 2,,7dpi40Hz 2,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:18|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165711aR1AL1A,M23165711aR1AL1A,7 xxx post injury+40Hz,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,7dpi40Hz_2_1.fq.gz 7dpi40Hz_2_2.fq.gz,fastq fastq,7457525100.0,24858417.0,7dpi40Hz 2 1.fq.gz,0:150 1:150,A:2040191437;C:1678135313;G:1713456206;T:2025700956;N:41188,150,150,,,2040191437,1678135313,1713456206,2025700956,41188,SRX23396544,SRS20257419,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30241,SRR27730918,SRX23396543,SRS20257418,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,7dpi40Hz+biological replicate 1,,7dpi40Hz 1,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:17|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165710aR1AL1A,M23165710aR1AL1A,7 xxx post injury+40Hz,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,7dpi40Hz_1_1.fq.gz 7dpi40Hz_1_2.fq.gz,fastq fastq,6855385800.0,22851286.0,7dpi40Hz 1 1.fq.gz,0:150 1:150,A:1880374717;C:1545013977;G:1569663640;T:1860295686;N:37780,150,150,,,1880374717,1545013977,1569663640,1860295686,37780,SRX23396543,SRS20257418,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30242,SRR27730919,SRX23396542,SRS20257417,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,7dpi+biological replicate 4,,7dpi 4,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:16|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165708aR1AL1A,M23165708aR1AL1A,7 xxx post injury,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,7dpi_4_1.fq.gz 7dpi_4_2.fq.gz,fastq fastq,6462470400.0,21541568.0,7dpi 4 1.fq.gz,0:150 1:150,A:1785795783;C:1441222995;G:1466593271;T:1768826748;N:31603,150,150,,,1785795783,1441222995,1466593271,1768826748,31603,SRX23396542,SRS20257417,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30243,SRR27730920,SRX23396541,SRS20257416,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,7dpi+biological replicate 3,,7dpi 3,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:15|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165706aR1AL1A,M23165706aR1AL1A,7 xxx post injury,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,7dpi_3_1.fq.gz 7dpi_3_2.fq.gz,fastq fastq,6710491200.0,22368304.0,7dpi 3 1.fq.gz,0:150 1:150,A:1831876501;C:1512529252;G:1544827061;T:1821200080;N:58306,150,150,,,1831876501,1512529252,1544827061,1821200080,58306,SRX23396541,SRS20257416,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30244,SRR27730921,SRX23396540,SRS20257415,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,7dpi+biological replicate 2,,7dpi 2,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:14|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165705aR1AL1A,M23165705aR1AL1A,7 xxx post injury,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,7dpi_2_1.fq.gz 7dpi_2_2.fq.gz,fastq fastq,6294917700.0,20983059.0,7dpi 2 1.fq.gz,0:150 1:150,A:1735431442;C:1394112982;G:1431966224;T:1733339379;N:67673,150,150,,,1735431442,1394112982,1431966224,1733339379,67673,SRX23396540,SRS20257415,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30245,SRR27730922,SRX23396539,SRS20257414,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,7dpi+biological replicate 1,,7dpi 1,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:13|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165704aR1AL1A,M23165704aR1AL1A,7 xxx post injury,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,7dpi_1_1.fq.gz 7dpi_1_2.fq.gz,fastq fastq,6694150800.0,22313836.0,7dpi 1 1.fq.gz,0:150 1:150,A:1824840998;C:1510909671;G:1543521247;T:1814842377;N:36507,150,150,,,1824840998,1510909671,1543521247,1814842377,36507,SRX23396539,SRS20257414,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30246,SRR27730923,SRX23396538,SRS20257413,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,4dpi40Hz+biological replicate 4,,4dpi40Hz 4,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:12|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165702aR1AL1A,M23165702aR1AL1A,4 xxx post injury+40Hz,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,4dpi40Hz_4_1.fq.gz 4dpi40Hz_4_2.fq.gz,fastq fastq,8672814300.0,28909381.0,4dpi40Hz 4 1.fq.gz,0:150 1:150,A:2372923011;C:1956760768;G:1989924842;T:2353159305;N:46374,150,150,,,2372923011,1956760768,1989924842,2353159305,46374,SRX23396538,SRS20257413,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30247,SRR27730924,SRX23396537,SRS20257412,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,4dpi40Hz+biological replicate 3,,4dpi40Hz 3,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:11|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165701aR1AL1A,M23165701aR1AL1A,4 xxx post injury+40Hz,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,4dpi40Hz_3_1.fq.gz 4dpi40Hz_3_2.fq.gz,fastq fastq,7566042300.0,25220141.0,4dpi40Hz 3 1.fq.gz,0:150 1:150,A:2073697374;C:1705150021;G:1733548148;T:2053605856;N:40901,150,150,,,2073697374,1705150021,1733548148,2053605856,40901,SRX23396537,SRS20257412,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30248,SRR27730925,SRX23396536,SRS20257411,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,Con+biological replicate 2,,Con 2,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165691aR1AL1A,M23165691aR1AL1A,Control,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,Con_2_1.fq.gz Con_2_2.fq.gz,fastq fastq,7211639400.0,24038798.0,Con 2 1.fq.gz,0:150 1:150,A:1979869383;C:1617364490;G:1649637969;T:1964729059;N:38499,150,150,,,1979869383,1617364490,1649637969,1964729059,38499,SRX23396536,SRS20257411,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30249,SRR27730926,SRX23396535,SRS20257410,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,Con+biological replicate 1,,Con 1,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165689aR1AL1A,M23165689aR1AL1A,Control,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,Con_1_1.fq.gz Con_1_2.fq.gz,fastq fastq,6217369800.0,20724566.0,Con 1 1.fq.gz,0:150 1:150,A:1714156006;C:1391042352;G:1415307378;T:1696831326;N:32738,150,150,,,1714156006,1391042352,1415307378,1696831326,32738,SRX23396535,SRS20257410,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
33304,SRR29927538,SRX25421512,SRS22081668,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,INL 3d rep2,MCWR 2019 000138,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:INL 3d rep2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury inner nuclear layer,INL 3d rep2,INL 3d rep2,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000138_S10_L001_R1_001.fastq.gz MCWR_2019_000138_S10_L001_R2_001.fastq.gz MCWR_2019_000138_S10_L002_R1_001.fastq.gz MCWR_2019_000138_S10_L002_R2_001.fastq.gz,fastq fastq fastq fastq,12792286105.0,42489107.0,MCWR 2019 000138 S10 L001 R1 001.fastq.gz,0:150.53 1:150.54,A:3362192057;C:3017281691;G:3072735924;T:3339916027;N:160406,150,150,,,3362192057,3017281691,3072735924,3339916027,160406,SRX25421512,SRS22081668,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.95023,0.94904,0.10306,0.10406,0.71167,0.71305,0.46929,0.47143,149,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33305,SRR29927539,SRX25421511,SRS22081667,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,INL 3d rep1,MCWR 2019 000137,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:INL 3d rep1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury inner nuclear layer,INL 3d rep1,INL 3d rep1,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000137_S9_L001_R1_001.fastq.gz MCWR_2019_000137_S9_L001_R2_001.fastq.gz MCWR_2019_000137_S9_L002_R1_001.fastq.gz MCWR_2019_000137_S9_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11290383949.0,37500632.0,MCWR 2019 000137 S9 L001 R1 001.fastq.gz,0:150.53 1:150.54,A:2978304239;C:2650227687;G:2709306614;T:2952404306;N:141103,150,150,,,2978304239,2650227687,2709306614,2952404306,141103,SRX25421511,SRS22081667,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.95037,0.94915,0.09395,0.0939,0.71019,0.71143,0.47425,0.46854,151,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33306,SRR29927540,SRX25421510,SRS22081666,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,INL Control rep3,MCWR 2019 000136,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:INL Control rep3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive inner nuclear layer,INL Control rep3,INL Control rep3,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000136_S8_L001_R1_001.fastq.gz MCWR_2019_000136_S8_L001_R2_001.fastq.gz MCWR_2019_000136_S8_L002_R1_001.fastq.gz MCWR_2019_000136_S8_L002_R2_001.fastq.gz,fastq fastq fastq fastq,10926876847.0,36289612.0,MCWR 2019 000136 S8 L001 R1 001.fastq.gz,0:150.54 1:150.56,A:2876719537;C:2534137531;G:2628404662;T:2887478941;N:136176,150,150,,,2876719537,2534137531,2628404662,2887478941,136176,SRX25421510,SRS22081666,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.9413,0.94085,0.12465,0.12554,0.71565,0.71536,0.47866,0.47866,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33307,SRR29927541,SRX25421509,SRS22081665,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,INL Control rep2,MCWR 2019 000135,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:INL Control rep2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive inner nuclear layer,INL Control rep2,INL Control rep2,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000135_S7_L001_R1_001.fastq.gz MCWR_2019_000135_S7_L001_R2_001.fastq.gz MCWR_2019_000135_S7_L002_R1_001.fastq.gz MCWR_2019_000135_S7_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11015573968.0,36586451.0,MCWR 2019 000135 S7 L001 R1 001.fastq.gz,0:150.54 1:150.54,A:2922133009;C:2558945272;G:2631247657;T:2903110333;N:137697,150,150,,,2922133009,2558945272,2631247657,2903110333,137697,SRX25421509,SRS22081665,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.94458,0.94452,0.1088,0.10943,0.71167,0.71161,0.48464,0.48393,149,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33308,SRR29927542,SRX25421508,SRS22081664,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,INL Control rep1,MCWR 2019 000134,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:INL Control rep1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive inner nuclear layer,INL Control rep1,INL Control rep1,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000134_S6_L001_R1_001.fastq.gz MCWR_2019_000134_S6_L001_R2_001.fastq.gz MCWR_2019_000134_S6_L002_R1_001.fastq.gz MCWR_2019_000134_S6_L002_R2_001.fastq.gz,fastq fastq fastq fastq,12065204348.0,40074475.0,MCWR 2019 000134 S6 L001 R1 001.fastq.gz,0:150.53 1:150.54,A:3229181479;C:2787700756;G:2849413410;T:3198752940;N:155763,150,150,,,3229181479,2787700756,2849413410,3198752940,155763,SRX25421508,SRS22081664,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.94249,0.94233,0.10755,0.10774,0.71427,0.71449,0.48361,0.48286,151,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33309,SRR29927543,SRX25421507,SRS22081663,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,GCL 3d rep3,MCWR 2019 000133,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:GCL 3d rep3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury ganglion cell layer,GCL 3d rep3,GCL 3d rep3,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000133_S5_L001_R1_001.fastq.gz MCWR_2019_000133_S5_L001_R2_001.fastq.gz MCWR_2019_000133_S5_L002_R1_001.fastq.gz MCWR_2019_000133_S5_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11567455830.0,38423805.0,MCWR 2019 000133 S5 L001 R1 001.fastq.gz,0:150.52 1:150.52,A:3334076845;C:2423637444;G:2488288638;T:3321309876;N:143027,150,150,,,3334076845,2423637444,2488288638,3321309876,143027,SRX25421507,SRS22081663,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.90351,0.90273,0.20071,0.20036,0.7443,0.74588,0.57805,0.58483,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33310,SRR29927544,SRX25421506,SRS22081662,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,GCL 3d rep2,MCWR 2019 000132,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:GCL 3d rep2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury ganglion cell layer,GCL 3d rep2,GCL 3d rep2,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000132_S4_L001_R1_001.fastq.gz MCWR_2019_000132_S4_L001_R2_001.fastq.gz MCWR_2019_000132_S4_L002_R1_001.fastq.gz MCWR_2019_000132_S4_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9928742591.0,32979607.0,MCWR 2019 000132 S4 L001 R1 001.fastq.gz,0:150.53 1:150.53,A:2670122365;C:2289339998;G:2333968379;T:2635186637;N:125212,150,150,,,2670122365,2289339998,2333968379,2635186637,125212,SRX25421506,SRS22081662,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.94453,0.9429,0.1039,0.10476,0.72032,0.72184,0.51703,0.51652,148,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33313,SRR29927547,SRX25421503,SRS22081659,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,GCL 3d rep1,MCWR 2019 000131,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:GCL 3d rep1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury ganglion cell layer,GCL 3d rep1,GCL 3d rep1,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000131_S3_L001_R1_001.fastq.gz MCWR_2019_000131_S3_L001_R2_001.fastq.gz MCWR_2019_000131_S3_L002_R1_001.fastq.gz MCWR_2019_000131_S3_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11040747879.0,36674133.0,MCWR 2019 000131 S3 L001 R1 001.fastq.gz,0:150.52 1:150.53,A:3033865749;C:2483236067;G:2540109846;T:2983395404;N:140813,150,150,,,3033865749,2483236067,2540109846,2983395404,140813,SRX25421503,SRS22081659,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.9328,0.93075,0.12255,0.12345,0.72675,0.72949,0.52776,0.53024,150,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33318,SRR29927552,SRX25421498,SRS22081654,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,ONL 3d rep3,MCWR 2019 000145,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:ONL 3d rep3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury outer nuclear layer,ONL 3d rep3,ONL 3d rep3,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000145_S16_L001_R1_001.fastq.gz MCWR_2019_000145_S16_L001_R2_001.fastq.gz MCWR_2019_000145_S16_L002_R1_001.fastq.gz MCWR_2019_000145_S16_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11434401733.0,37973868.0,MCWR 2019 000145 S16 L001 R1 001.fastq.gz,0:150.56 1:150.55,A:2952068036;C:2779158705;G:2786796140;T:2916234156;N:144696,150,150,,,2952068036,2779158705,2786796140,2916234156,144696,SRX25421498,SRS22081654,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.95416,0.95385,0.07766,0.07806,0.79024,0.78989,0.40138,0.42872,150,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33319,SRR29927553,SRX25421497,SRS22081653,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,ONL 3d rep2,MCWR 2019 000144,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:ONL 3d rep2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury outer nuclear layer,ONL 3d rep2,ONL 3d rep2,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000144_S15_L002_R2_001.fastq.gz MCWR_2019_000144_S15_L002_R1_001.fastq.gz MCWR_2019_000144_S15_L001_R2_001.fastq.gz MCWR_2019_000144_S15_L001_R1_001.fastq.gz,fastq fastq fastq fastq,10784131193.0,35816254.0,MCWR 2019 000144 S15 L001 R1 001.fastq.gz,0:150.55 1:150.55,A:2770521598;C:2622163802;G:2642603869;T:2748709177;N:132747,150,150,,,2770521598,2622163802,2642603869,2748709177,132747,SRX25421497,SRS22081653,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.95823,0.9574,0.06867,0.06894,0.77055,0.77234,0.43067,0.43052,149,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33320,SRR29927554,SRX25421496,SRS22081652,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,ONL 3d rep1,MCWR 2019 000143,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:ONL 3d rep1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury outer nuclear layer,ONL 3d rep1,ONL 3d rep1,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000143_S14_L001_R1_001.fastq.gz MCWR_2019_000143_S14_L001_R2_001.fastq.gz MCWR_2019_000143_S14_L002_R1_001.fastq.gz MCWR_2019_000143_S14_L002_R2_001.fastq.gz,fastq fastq fastq fastq,10414222985.0,34587231.0,MCWR 2019 000143 S14 L001 R1 001.fastq.gz,0:150.55 1:150.55,A:2640548677;C:2562227240;G:2582839755;T:2628478265;N:129048,150,150,,,2640548677,2562227240,2582839755,2628478265,129048,SRX25421496,SRS22081652,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.95893,0.95898,0.06693,0.06725,0.78216,0.7833,0.41018,0.40065,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33321,SRR29927555,SRX25421495,SRS22081651,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,ONL Control rep3,MCWR 2019 000142,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:ONL Control rep3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive outer nuclear layer,ONL Control rep3,ONL Control rep3,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000142_S13_L001_R1_001.fastq.gz MCWR_2019_000142_S13_L001_R2_001.fastq.gz MCWR_2019_000142_S13_L002_R1_001.fastq.gz MCWR_2019_000142_S13_L002_R2_001.fastq.gz,fastq fastq fastq fastq,10611460744.0,35241917.0,MCWR 2019 000142 S13 L001 R1 001.fastq.gz,0:150.55 1:150.55,A:2729659216;C:2572974863;G:2597112533;T:2711584081;N:130051,150,150,,,2729659216,2572974863,2597112533,2711584081,130051,SRX25421495,SRS22081651,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.95524,0.95438,0.08233,0.08236,0.76654,0.76682,0.41657,0.41626,151,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33322,SRR29927556,SRX25421494,SRS22081650,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,ONL Control rep2,MCWR 2019 000141,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:ONL Control rep2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive outer nuclear layer,ONL Control rep2,ONL Control rep2,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000141_S12_L001_R1_001.fastq.gz MCWR_2019_000141_S12_L001_R2_001.fastq.gz MCWR_2019_000141_S12_L002_R1_001.fastq.gz MCWR_2019_000141_S12_L002_R2_001.fastq.gz,fastq fastq fastq fastq,12296763008.0,40838426.0,MCWR 2019 000141 S12 L001 R1 001.fastq.gz,0:150.55 1:150.55,A:3157494503;C:2976873172;G:3025100891;T:3137136259;N:158183,150,150,,,3157494503,2976873172,3025100891,3137136259,158183,SRX25421494,SRS22081650,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.9531,0.95203,0.08284,0.08254,0.76816,0.76879,0.40735,0.41583,150,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33323,SRR29927557,SRX25421493,SRS22081649,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,ONL Control rep1,MCWR 2019 000140,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:ONL Control rep1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive outer nuclear layer,ONL Control rep1,ONL Control rep1,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000140_S11_L001_R1_001.fastq.gz MCWR_2019_000140_S11_L001_R2_001.fastq.gz MCWR_2019_000140_S11_L002_R1_001.fastq.gz MCWR_2019_000140_S11_L002_R2_001.fastq.gz,fastq fastq fastq fastq,12797441059.0,42498374.0,MCWR 2019 000140 S11 L001 R1 001.fastq.gz,0:150.56 1:150.56,A:3214435348;C:3160301138;G:3218337754;T:3204200743;N:166076,150,150,,,3214435348,3160301138,3218337754,3204200743,166076,SRX25421493,SRS22081649,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.95836,0.95804,0.0672,0.06787,0.79255,0.7933,0.37626,0.37493,149,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33324,SRR29927558,SRX25421492,SRS22081648,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,GCL Control rep2,MCWR 2019 000129,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:GCL Control rep2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive ganglion cell layer,GCL Control rep2,GCL Control rep2,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000129_S2_L001_R1_001.fastq.gz MCWR_2019_000129_S2_L001_R2_001.fastq.gz MCWR_2019_000129_S2_L002_R1_001.fastq.gz MCWR_2019_000129_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9904585990.0,32898356.0,MCWR 2019 000129 S2 L001 R1 001.fastq.gz,0:150.53 1:150.54,A:2686769990;C:2251531625;G:2320304039;T:2645855407;N:124929,150,150,,,2686769990,2251531625,2320304039,2645855407,124929,SRX25421492,SRS22081648,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.93013,0.93029,0.10617,0.10657,0.74712,0.74757,0.56746,0.56517,150,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33325,SRR29927559,SRX25421491,SRS22081647,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,GCL Control rep1,MCWR 2019 000128,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:male|tissue:retina|treatment:GCL Control rep1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive ganglion cell layer,GCL Control rep1,GCL Control rep1,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000128_S1_L001_R1_001.fastq.gz MCWR_2019_000128_S1_L001_R2_001.fastq.gz MCWR_2019_000128_S1_L002_R1_001.fastq.gz MCWR_2019_000128_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11199698460.0,37200254.0,MCWR 2019 000128 S1 L001 R1 001.fastq.gz,0:150.53 1:150.53,A:3065207886;C:2519670393;G:2596314938;T:3018365726;N:139517,150,150,,,3065207886,2519670393,2596314938,3018365726,139517,SRX25421491,SRS22081647,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.93213,0.93206,0.13073,0.13125,0.7305,0.73079,0.5518,0.55133,149,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System
33379,SRR30184285,SRX25650011,SRS22293080,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,cMO 2,wt cmo2 M,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:male|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:cMO 2|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L10,L10,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L10_S128_L005_R2_001.fastq.gz L10_S128_L005_R1_001.fastq.gz,fastq fastq,20328275944.0,67312172.0,L10 S128 L005 R1 001.fastq.gz,0:151 1:151,A:5643585269;C:4447562096;G:4432908344;T:5802780590;N:1439645,151,151,,,5643585269,4447562096,4432908344,5802780590,1439645,SRX25650011,SRS22293080,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.89472,0.89558,0.14231,0.14209,0.76359,0.76327,0.57442,0.57155,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33380,SRR30184286,SRX25650010,SRS22293078,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,cMO 1,wt cmo1 M,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:male|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:cMO 1|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L09,L09,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L09_S106_L004_R2_001.fastq.gz L09_S106_L004_R1_001.fastq.gz,fastq fastq,17931167252.0,59374726.0,L09 S106 L004 R1 001.fastq.gz,0:151 1:151,A:4724456408;C:4170780589;G:4192052775;T:4841803749;N:2073731,151,151,,,4724456408,4170780589,4192052775,4841803749,2073731,SRX25650010,SRS22293078,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.92527,0.92522,0.05941,0.05976,0.76532,0.76583,0.55358,0.55497,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33381,SRR30184287,SRX25650009,SRS22293079,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,3dpi 4,wt R2 F,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:female|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:3dpi 4|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L08,L08,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L08_S127_L005_R2_001.fastq.gz L08_S127_L005_R1_001.fastq.gz,fastq fastq,22665495016.0,75051308.0,L08 S127 L005 R1 001.fastq.gz,0:151 1:151,A:6228385739;C:4990124759;G:4979460238;T:6465924079;N:1600201,151,151,,,6228385739,4990124759,4979460238,6465924079,1600201,SRX25650009,SRS22293079,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.87648,0.87921,0.12966,0.13019,0.75627,0.75666,0.5783,0.5754,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33382,SRR30184288,SRX25650008,SRS22293077,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,3dpi 3,wt R1 F,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:female|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:3dpi 3|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L07,L07,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L07_S126_L005_R2_001.fastq.gz L07_S126_L005_R1_001.fastq.gz,fastq fastq,22406825976.0,74194788.0,L07 S126 L005 R1 001.fastq.gz,0:151 1:151,A:6090398182;C:4986126981;G:5056253833;T:6272474188;N:1572792,151,151,,,6090398182,4986126981,5056253833,6272474188,1572792,SRX25650008,SRS22293077,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.9153,0.91559,0.10005,0.0998,0.74679,0.7469,0.53845,0.5395,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33383,SRR30184289,SRX25650007,SRS22293075,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,3dpi 2,wt R2 M,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:male|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:3dpi 2|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L06,L06,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L06_S125_L005_R2_001.fastq.gz L06_S125_L005_R1_001.fastq.gz,fastq fastq,21918766796.0,72578698.0,L06 S125 L005 R1 001.fastq.gz,0:151 1:151,A:6030044320;C:4788979368;G:4790388904;T:6307807807;N:1546397,151,151,,,6030044320,4788979368,4790388904,6307807807,1546397,SRX25650007,SRS22293075,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.87272,0.87475,0.15184,0.15299,0.76777,0.76702,0.58094,0.57863,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33384,SRR30184290,SRX25650006,SRS22293076,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,3dpi 1,wt R1 M,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:male|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:3dpi 1|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L05,L05,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L05_S124_L005_R1_001.fastq.gz L05_S124_L005_R2_001.fastq.gz,fastq fastq,20254563180.0,67068090.0,L05 S124 L005 R1 001.fastq.gz,0:151 1:151,A:5433584775;C:4559357895;G:4610242789;T:5649933621;N:1444100,151,151,,,5433584775,4559357895,4610242789,5649933621,1444100,SRX25650006,SRS22293076,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.90628,0.90764,0.08395,0.08422,0.7712,0.77086,0.5176,0.51705,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33385,SRR30184291,SRX25650005,SRS22293074,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,uninjured 4,wt L2 F,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:female|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:uninjured 4|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L04,L04,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L04_S142_L006_R2_001.fastq.gz L04_S142_L006_R1_001.fastq.gz,fastq fastq,29812977034.0,98718467.0,L04 S142 L006 R1 001.fastq.gz,0:151 1:151,A:8014887204;C:6674942655;G:6635556218;T:8483149485;N:4441472,151,151,,,8014887204,6674942655,6635556218,8483149485,4441472,SRX25650005,SRS22293074,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.84638,0.84891,0.16019,0.1609,0.77737,0.77733,0.62585,0.63219,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33386,SRR30184292,SRX25650004,SRS22293073,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,heatshock srebf2MO 4,hs smo2 F,,strain:Tghsp70l:nSrebf2 2AmCherry  cmcl2:EGFP|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:female|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:heatshock srebf2MO 4|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L28,L28,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L28_S116_L004_R2_001.fastq.gz L28_S116_L004_R1_001.fastq.gz,fastq fastq,17026943012.0,56380606.0,L28 S116 L004 R1 001.fastq.gz,0:151 1:151,A:4669306614;C:3826935006;G:3777947200;T:4750777220;N:1976972,151,151,,,4669306614,3826935006,3777947200,4750777220,1976972,SRX25650004,SRS22293073,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.93284,0.93235,0.07802,0.07812,0.75568,0.75597,0.55431,0.54921,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33387,SRR30184293,SRX25650003,SRS22293072,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,heatshock srebf2MO 3,hs smo1 F,,strain:Tghsp70l:nSrebf2 2AmCherry  cmcl2:EGFP|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:female|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:heatshock srebf2MO 3|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L27,L27,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L27_S115_L004_R2_001.fastq.gz L27_S115_L004_R1_001.fastq.gz,fastq fastq,22610315690.0,74868595.0,L27 S115 L004 R1 001.fastq.gz,0:151 1:151,A:6205491974;C:5075129196;G:4965212019;T:6361870398;N:2612103,151,151,,,6205491974,5075129196,4965212019,6361870398,2612103,SRX25650003,SRS22293072,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.78769,0.78807,0.09282,0.09299,0.76619,0.7651,0.54884,0.5509,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33388,SRR30184294,SRX25650002,SRS22293071,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,heatshock srebf2MO 2,hs smo2 M,,strain:Tghsp70l:nSrebf2 2AmCherry  cmcl2:EGFP|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:male|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:heatshock srebf2MO 2|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L26,L26,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L26_S144_L006_R2_001.fastq.gz L26_S144_L006_R1_001.fastq.gz,fastq fastq,17129465368.0,56720084.0,L26 S144 L006 R1 001.fastq.gz,0:151 1:151,A:4750698191;C:3734802838;G:3895289691;T:4746170435;N:2504213,151,151,,,4750698191,3734802838,3895289691,4746170435,2504213,SRX25650002,SRS22293071,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.93654,0.92792,0.07609,0.07622,0.75061,0.75357,0.52583,0.53272,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33389,SRR30184295,SRX25650001,SRS22293070,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,heatshock srebf2MO 1,hs smo1 M,,strain:Tghsp70l:nSrebf2 2AmCherry  cmcl2:EGFP|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:male|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:heatshock srebf2MO 1|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L25,L25,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L25_S114_L004_R2_001.fastq.gz L25_S114_L004_R1_001.fastq.gz,fastq fastq,18411870316.0,60966458.0,L25 S114 L004 R1 001.fastq.gz,0:151 1:151,A:5037571347;C:4144572498;G:4103153869;T:5124440844;N:2131758,151,151,,,5037571347,4144572498,4103153869,5124440844,2131758,SRX25650001,SRS22293070,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.92822,0.92792,0.0886,0.08918,0.75974,0.75978,0.55638,0.55618,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33390,SRR30184296,SRX25650000,SRS22293066,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,uninjured 3,wt L1 F,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:female|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:uninjured 3|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L03,L03,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L03_S105_L004_R1_001.fastq.gz L03_S105_L004_R2_001.fastq.gz,fastq fastq,19718182792.0,65291996.0,L03 S105 L004 R1 001.fastq.gz,0:151 1:151,A:5247234351;C:4504410887;G:4526181297;T:5438074144;N:2282113,151,151,,,5247234351,4504410887,4526181297,5438074144,2282113,SRX25650000,SRS22293066,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.90475,0.90699,0.11305,0.11331,0.75014,0.74929,0.52801,0.54316,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33391,SRR30184297,SRX25649999,SRS22293069,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,heatshock cMO 4,hs cmo2 F,,strain:Tghsp70l:nSrebf2 2AmCherry  cmcl2:EGFP|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:female|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:heatshock cMO 4|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L24,L24,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L24_S134_L005_R2_001.fastq.gz L24_S134_L005_R1_001.fastq.gz,fastq fastq,19377661484.0,64164442.0,L24 S134 L005 R1 001.fastq.gz,0:151 1:151,A:5371834087;C:4284931090;G:4227428342;T:5492109103;N:1358862,151,151,,,5371834087,4284931090,4227428342,5492109103,1358862,SRX25649999,SRS22293069,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.9104,0.90922,0.11083,0.11062,0.75325,0.7543,0.54602,0.54303,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33392,SRR30184298,SRX25649998,SRS22293067,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,heatshock cMO 3,hs cmo1 F,,strain:Tghsp70l:nSrebf2 2AmCherry  cmcl2:EGFP|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:female|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:heatshock cMO 3|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L23,L23,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L23_S143_L006_R2_001.fastq.gz L23_S143_L006_R1_001.fastq.gz,fastq fastq,28079439956.0,92978278.0,L23 S143 L006 R1 001.fastq.gz,0:151 1:151,A:7811720040;C:6084170964;G:6064272363;T:8115079585;N:4197004,151,151,,,7811720040,6084170964,6064272363,8115079585,4197004,SRX25649998,SRS22293067,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.86593,0.86525,0.14584,0.14587,0.77498,0.77433,0.59534,0.59433,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33393,SRR30184299,SRX25649997,SRS22293068,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,heatshock cMO 2,hs cmo2 M,,strain:Tghsp70l:nSrebf2 2AmCherry  cmcl2:EGFP|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:male|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:heatshock cMO 2|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L22,L22,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L22_S133_L005_R2_001.fastq.gz L22_S133_L005_R1_001.fastq.gz,fastq fastq,20494382588.0,67862194.0,L22 S133 L005 R1 001.fastq.gz,0:151 1:151,A:5610165229;C:4583590395;G:4590759271;T:5708435247;N:1432446,151,151,,,5610165229,4583590395,4590759271,5708435247,1432446,SRX25649997,SRS22293068,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.92306,0.92279,0.0879,0.08765,0.7671,0.76579,0.56402,0.56401,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33394,SRR30184300,SRX25649996,SRS22293064,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,heatshock cMO 1,hs cmo1 M,,strain:Tghsp70l:nSrebf2 2AmCherry  cmcl2:EGFP|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:male|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:heatshock cMO 1|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L21,L21,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L21_S113_L004_R1_001.fastq.gz L21_S113_L004_R2_001.fastq.gz,fastq fastq,22282038670.0,73781585.0,L21 S113 L004 R1 001.fastq.gz,0:151 1:151,A:5984432885;C:5103219794;G:5123288852;T:6068507910;N:2589229,151,151,,,5984432885,5103219794,5123288852,6068507910,2589229,SRX25649996,SRS22293064,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.93523,0.93442,0.06557,0.06558,0.76463,0.76532,0.54365,0.53711,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33395,SRR30184301,SRX25649995,SRS22293061,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,srebf2MO 4,wt smo2 F,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:female|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:srebf2MO 4|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L16,L16,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L16_S108_L004_R1_001.fastq.gz L16_S108_L004_R2_001.fastq.gz,fastq fastq,25364244630.0,83987565.0,L16 S108 L004 R1 001.fastq.gz,0:151 1:151,A:6783811492;C:5825885841;G:5791188806;T:6960421955;N:2936536,151,151,,,6783811492,5825885841,5791188806,6960421955,2936536,SRX25649995,SRS22293061,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.93174,0.93131,0.06871,0.06898,0.75461,0.75386,0.54103,0.54073,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33396,SRR30184302,SRX25649994,SRS22293065,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,srebf2MO 3,wt smo1 F,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:female|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:srebf2MO 3|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L15,L15,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L15_S132_L005_R2_001.fastq.gz L15_S132_L005_R1_001.fastq.gz,fastq fastq,24643120876.0,81599738.0,L15 S132 L005 R1 001.fastq.gz,0:151 1:151,A:6791560596;C:5441282614;G:5412453327;T:6996084050;N:1740289,151,151,,,6791560596,5441282614,5412453327,6996084050,1740289,SRX25649994,SRS22293065,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.90806,0.90874,0.11049,0.11033,0.75885,0.75741,0.54345,0.55215,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33397,SRR30184303,SRX25649993,SRS22293062,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,srebf2MO 2,wt smo2 M,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:male|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:srebf2MO 2|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L14,L14,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L14_S131_L005_R2_001.fastq.gz L14_S131_L005_R1_001.fastq.gz,fastq fastq,20984328060.0,69484530.0,L14 S131 L005 R1 001.fastq.gz,0:151 1:151,A:5728503785;C:4710613293;G:4687638412;T:5856111147;N:1461423,151,151,,,5728503785,4710613293,4687638412,5856111147,1461423,SRX25649993,SRS22293062,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.92516,0.92471,0.08416,0.08435,0.76568,0.76585,0.56286,0.56146,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33398,SRR30184304,SRX25649992,SRS22293059,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,srebf2MO 1,wt smo1 M,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:male|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:srebf2MO 1|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L13,L13,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L13_S130_L005_R1_001.fastq.gz L13_S130_L005_R2_001.fastq.gz,fastq fastq,17976563590.0,59525045.0,L13 S130 L005 R1 001.fastq.gz,0:151 1:151,A:4931490430;C:3978811459;G:3956968246;T:5108014615;N:1278840,151,151,,,4931490430,3978811459,3956968246,5108014615,1278840,SRX25649992,SRS22293059,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.8948,0.89491,0.13113,0.13061,0.76254,0.76246,0.57407,0.57069,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33399,SRR30184305,SRX25649991,SRS22293060,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,cMO 4,wt cmo2 F,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:female|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:cMO 4|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L12,L12,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L12_S129_L005_R2_001.fastq.gz L12_S129_L005_R1_001.fastq.gz,fastq fastq,19905894214.0,65913557.0,L12 S129 L005 R1 001.fastq.gz,0:151 1:151,A:5382577098;C:4496451576;G:4493042842;T:5532424959;N:1397739,151,151,,,5382577098,4496451576,4493042842,5532424959,1397739,SRX25649991,SRS22293060,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.9238,0.92347,0.08792,0.08777,0.75933,0.75921,0.56478,0.567,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33400,SRR30184306,SRX25649990,SRS22293063,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,cMO 3,wt cmo1 F,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:female|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:cMO 3|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L11,L11,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L11_S107_L004_R1_001.fastq.gz L11_S107_L004_R2_001.fastq.gz,fastq fastq,17297093488.0,57275144.0,L11 S107 L004 R1 001.fastq.gz,0:151 1:151,A:4727002988;C:3860128821;G:3837802284;T:4870157333;N:2002062,151,151,,,4727002988,3860128821,3837802284,4870157333,2002062,SRX25649990,SRS22293063,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.86746,0.86798,0.10604,0.1069,0.76396,0.7639,0.56148,0.55457,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33401,SRR30184307,SRX25649989,SRS22293058,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,uninjured 2,wt L2 M,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:male|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:uninjured 2|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L02,L02,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L02_S141_L006_R2_001.fastq.gz L02_S141_L006_R1_001.fastq.gz,fastq fastq,24399093702.0,80791701.0,L02 S141 L006 R1 001.fastq.gz,0:151 1:151,A:6567405598;C:5419524814;G:5626869131;T:6781638199;N:3655960,151,151,,,6567405598,5419524814,5626869131,6781638199,3655960,SRX25649989,SRS22293058,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.88324,0.88428,0.12546,0.12616,0.77141,0.77021,0.58483,0.58455,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
33402,SRR30184308,SRX25649988,SRS22293057,SRP525334,PRJNA1145997,Regulation of optic nerve regeneration by srebf2,PRJNA1145997,Other,Laser capture microdissection of the retinal ganglion cell layer followed by mRNA seq was used to measure differentially expressed genes in adult zebrafish at three days post optic nerve crush injury. Experimental groups include naive control  nonspecific morpholino control  morpholino mediated srebf2 gene knockdown  nonspecific morpholino control plus daily heat shock in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish  and morpholino mediated srebf2 gene knockdown in Tghsp70l:nSrebf2 2AmCherry  cmlc2:EGFP fish with daily heatshock. These data provide a resource to study the effects of srebf2 manipulation on transcriptomic responses to optic nerve injury in the adult zebrafish model.,,,,uninjured 1,wt L1 M,,strain:wild type|age:>3 month|collection date:2023 11 06|geo loc name:USA: Milwaukee  WI|sex:male|tissue:retinal ganglion cell layer|biomaterial provider:Matthew B. Veldman  Medical College of Wisconsin|treatment:uninjured 1|BioSampleModel:Model organism or animal,,,,,,,,,LCM seq of Danio rerio:retinal ganglion cell layer,L01,L01,LCM seq  NucleoSpin RNA XS purified  ultra low input RNAseq at Novogene,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP525334,,,L01_S123_L005_R2_001.fastq.gz L01_S123_L005_R1_001.fastq.gz,fastq fastq,17596481188.0,58266494.0,L01 S123 L005 R1 001.fastq.gz,0:151 1:151,A:4773806012;C:3941529807;G:3951952531;T:4927955026;N:1237812,151,151,,,4773806012,3941529807,3951952531,4927955026,1237812,SRX25649988,SRS22293057,SRA1943640,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.9124,0.91249,0.10052,0.10034,0.76751,0.76773,0.58532,0.58581,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-08-09,Adult,Adult,Eye,Sensory System
34447,SRR31768861,SRX27130600,SRS23587604,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #3,GSM8691385,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #3,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7,GSM8691385,GSM8691385: adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #3; Danio rerio; RNA Seq,GSM8691385 r1,GSM8691385,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,7DPI_uninjured_03_S30_R1_001.fastq.gz 7DPI_uninjured_03_S30_R2_001.fastq.gz,fastq fastq,5698047024.0,29362783.0,GSM8691385 r1,0:97.02 1:97.03,A:1667059209;C:1124020328;G:1186053751;T:1719272359;N:1641377,97,97,,,1667059209,1124020328,1186053751,1719272359,1641377,SRX27130600,SRS23587604,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34448,SRR31768862,SRX27130599,SRS23587603,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #2,GSM8691384,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #2,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7,GSM8691384,GSM8691384: adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #2; Danio rerio; RNA Seq,GSM8691384 r1,GSM8691384,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,7DPI_uninjured_02_S29_R1_001.fastq.gz 7DPI_uninjured_02_S29_R2_001.fastq.gz,fastq fastq,6167521979.0,31682719.0,GSM8691384 r1,0:97.33 1:97.33,A:1801911913;C:1219391300;G:1283420442;T:1861159517;N:1638807,97,97,,,1801911913,1219391300,1283420442,1861159517,1638807,SRX27130599,SRS23587603,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34449,SRR31768863,SRX27130598,SRS23587602,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #1,GSM8691383,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #1,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7,GSM8691383,GSM8691383: adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #1; Danio rerio; RNA Seq,GSM8691383 r1,GSM8691383,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,7DPI_uninjured_01_S28_R1_001.fastq.gz 7DPI_uninjured_01_S28_R2_001.fastq.gz,fastq fastq,6017592709.0,30979971.0,GSM8691383 r1,0:97.12 1:97.12,A:1777015201;C:1171009321;G:1236169034;T:1831770286;N:1628867,97,97,,,1777015201,1171009321,1236169034,1831770286,1628867,SRX27130598,SRS23587602,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34450,SRR31768864,SRX27130597,SRS23587601,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #3,GSM8691382,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #3,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691382,GSM8691382: adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #3; Danio rerio; RNA Seq,GSM8691382 r1,GSM8691382,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,7DPI_injured_03_S27_R1_001.fastq.gz 7DPI_injured_03_S27_R2_001.fastq.gz,fastq fastq,6341961565.0,32524944.0,GSM8691382 r1,0:97.49 1:97.49,A:1851283556;C:1264914896;G:1328636652;T:1895553719;N:1572742,97,97,,,1851283556,1264914896,1328636652,1895553719,1572742,SRX27130597,SRS23587601,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34451,SRR31768865,SRX27130596,SRS23587600,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #2,GSM8691381,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #2,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691381,GSM8691381: adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #2; Danio rerio; RNA Seq,GSM8691381 r1,GSM8691381,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,7DPI_injured_02_S26_R1_001.fastq.gz 7DPI_injured_02_S26_R2_001.fastq.gz,fastq fastq,6235870535.0,31994279.0,GSM8691381 r1,0:97.45 1:97.46,A:1822480684;C:1235794789;G:1300588308;T:1875414630;N:1592124,97,97,,,1822480684,1235794789,1300588308,1875414630,1592124,SRX27130596,SRS23587600,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34452,SRR31768866,SRX27130595,SRS23587599,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #1,GSM8691380,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #1,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691380,GSM8691380: adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #1; Danio rerio; RNA Seq,GSM8691380 r1,GSM8691380,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,7DPI_injured_01_S25_R1_001.fastq.gz 7DPI_injured_01_S25_R2_001.fastq.gz,fastq fastq,6174385200.0,31622915.0,GSM8691380 r1,0:97.62 1:97.63,A:1787576071;C:1247968531;G:1306271111;T:1831148003;N:1421484,97,97,,,1787576071,1247968531,1306271111,1831148003,1421484,SRX27130595,SRS23587599,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34453,SRR31768867,SRX27130594,SRS23587598,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #3,GSM8691379,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 5|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #3,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 5,GSM8691379,GSM8691379: adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #3; Danio rerio; RNA Seq,GSM8691379 r1,GSM8691379,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,5DPI_uninjured_03_S24_R1_001.fastq.gz 5DPI_uninjured_03_S24_R2_001.fastq.gz,fastq fastq,6412343629.0,34154945.0,GSM8691379 r1,0:93.86 1:93.88,A:1885512926;C:1263616925;G:1311969388;T:1947630859;N:3613531,93,93,,,1885512926,1263616925,1311969388,1947630859,3613531,SRX27130594,SRS23587598,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34454,SRR31768868,SRX27130593,SRS23587597,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #2,GSM8691378,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 5|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #2,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 5,GSM8691378,GSM8691378: adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #2; Danio rerio; RNA Seq,GSM8691378 r1,GSM8691378,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,5DPI_uninjured_02_S23_R1_001.fastq.gz 5DPI_uninjured_02_S23_R2_001.fastq.gz,fastq fastq,6672888700.0,34007957.0,GSM8691378 r1,0:98.11 1:98.11,A:1934192871;C:1346688691;G:1405041934;T:1985769861;N:1195343,98,98,,,1934192871,1346688691,1405041934,1985769861,1195343,SRX27130593,SRS23587597,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34455,SRR31768869,SRX27130592,SRS23587596,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #1,GSM8691377,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 5|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #1,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 5,GSM8691377,GSM8691377: adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #1; Danio rerio; RNA Seq,GSM8691377 r1,GSM8691377,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,5DPI_uninjured_01_S22_R1_001.fastq.gz 5DPI_uninjured_01_S22_R2_001.fastq.gz,fastq fastq,6710121204.0,35640240.0,GSM8691377 r1,0:94.13 1:94.14,A:1930817182;C:1378539334;G:1418299809;T:1979047683;N:3417196,94,94,,,1930817182,1378539334,1418299809,1979047683,3417196,SRX27130592,SRS23587596,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34456,SRR31768870,SRX27130591,SRS23587595,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #3,GSM8691376,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #3,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691376,GSM8691376: adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #3; Danio rerio; RNA Seq,GSM8691376 r1,GSM8691376,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,5DPI_injured_03_S21_R1_001.fastq.gz 5DPI_injured_03_S21_R2_001.fastq.gz,fastq fastq,5815478166.0,29829330.0,GSM8691376 r1,0:97.47 1:97.49,A:1686233316;C:1173233216;G:1223299576;T:1731320900;N:1391158,97,97,,,1686233316,1173233216,1223299576,1731320900,1391158,SRX27130591,SRS23587595,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34457,SRR31768871,SRX27130590,SRS23587594,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #2,GSM8691375,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #2,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691375,GSM8691375: adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #2; Danio rerio; RNA Seq,GSM8691375 r1,GSM8691375,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,5DPI_injured_02_S20_R1_001.fastq.gz 5DPI_injured_02_S20_R2_001.fastq.gz,fastq fastq,6463184463.0,33031735.0,GSM8691375 r1,0:97.83 1:97.84,A:1869116597;C:1303631450;G:1365056296;T:1924007964;N:1372156,97,97,,,1869116597,1303631450,1365056296,1924007964,1372156,SRX27130590,SRS23587594,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34458,SRR31768872,SRX27130589,SRS23587593,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #1,GSM8691374,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #1,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691374,GSM8691374: adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #1; Danio rerio; RNA Seq,GSM8691374 r1,GSM8691374,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,5DPI_injured_01_S19_R1_001.fastq.gz 5DPI_injured_01_S19_R2_001.fastq.gz,fastq fastq,5770277062.0,29421167.0,GSM8691374 r1,0:98.06 1:98.07,A:1659818839;C:1176285041;G:1230578027;T:1702467577;N:1127578,98,98,,,1659818839,1176285041,1230578027,1702467577,1127578,SRX27130589,SRS23587593,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34459,SRR31768873,SRX27130588,SRS23587592,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #3,GSM8691373,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #3,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1,GSM8691373,GSM8691373: adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #3; Danio rerio; RNA Seq,GSM8691373 r1,GSM8691373,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,1DPI_uninjured_03_S18_R1_001.fastq.gz 1DPI_uninjured_03_S18_R2_001.fastq.gz,fastq fastq,6268800701.0,32414990.0,GSM8691373 r1,0:96.68 1:96.71,A:1808208631;C:1259950394;G:1326103117;T:1872600468;N:1938091,96,96,,,1808208631,1259950394,1326103117,1872600468,1938091,SRX27130588,SRS23587592,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34460,SRR31768874,SRX27130587,SRS23587591,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #2,GSM8691372,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #2,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1,GSM8691372,GSM8691372: adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #2; Danio rerio; RNA Seq,GSM8691372 r1,GSM8691372,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,1DPI_uninjured_02_S17_R1_001.fastq.gz 1DPI_uninjured_02_S17_R2_001.fastq.gz,fastq fastq,6475037338.0,33641146.0,GSM8691372 r1,0:96.23 1:96.24,A:1875658518;C:1291113851;G:1361172356;T:1944790051;N:2302562,96,96,,,1875658518,1291113851,1361172356,1944790051,2302562,SRX27130587,SRS23587591,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34461,SRR31768875,SRX27130586,SRS23587590,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #1,GSM8691371,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #1,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1,GSM8691371,GSM8691371: adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #1; Danio rerio; RNA Seq,GSM8691371 r1,GSM8691371,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,1DPI_uninjured_01_S16_R1_001.fastq.gz 1DPI_uninjured_01_S16_R2_001.fastq.gz,fastq fastq,6400897196.0,33022714.0,GSM8691371 r1,0:96.92 1:96.91,A:1846404518;C:1284124731;G:1356841105;T:1911572894;N:1953948,96,96,,,1846404518,1284124731,1356841105,1911572894,1953948,SRX27130586,SRS23587590,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34462,SRR31768876,SRX27130585,SRS23587589,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #3,GSM8691370,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #3,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691370,GSM8691370: adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #3; Danio rerio; RNA Seq,GSM8691370 r1,GSM8691370,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,1DPI_injured_03_S15_R1_001.fastq.gz 1DPI_injured_03_S15_R2_001.fastq.gz,fastq fastq,5946459133.0,30587969.0,GSM8691370 r1,0:97.20 1:97.21,A:1716543360;C:1195543685;G:1259830252;T:1772896957;N:1644879,97,97,,,1716543360,1195543685,1259830252,1772896957,1644879,SRX27130585,SRS23587589,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34463,SRR31768877,SRX27130584,SRS23587588,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #2,GSM8691369,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #2,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691369,GSM8691369: adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #2; Danio rerio; RNA Seq,GSM8691369 r1,GSM8691369,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,1DPI_injured_02_S14_R1_001.fastq.gz 1DPI_injured_02_S14_R2_001.fastq.gz,fastq fastq,6366392345.0,32994721.0,GSM8691369 r1,0:96.48 1:96.47,A:1861203729;C:1243094742;G:1336477656;T:1923087937;N:2528281,96,96,,,1861203729,1243094742,1336477656,1923087937,2528281,SRX27130584,SRS23587588,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34464,SRR31768878,SRX27130583,SRS23587587,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #1,GSM8691368,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #1,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691368,GSM8691368: adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #1; Danio rerio; RNA Seq,GSM8691368 r1,GSM8691368,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,1DPI_injured_01_S13_R1_001.fastq.gz 1DPI_injured_01_S13_R2_001.fastq.gz,fastq fastq,6378025205.0,33385333.0,GSM8691368 r1,0:95.51 1:95.53,A:1875735808;C:1227743564;G:1334467564;T:1936726852;N:3351417,95,95,,,1875735808,1227743564,1334467564,1936726852,3351417,SRX27130583,SRS23587587,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34465,SRR31769117,SRX27130830,SRS23587817,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #3,GSM8691398,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #3,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7,GSM8691398,GSM8691398: adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #3; Danio rerio; RNA Seq,GSM8691398 r1,GSM8691398,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Uninjured-7DPI-3_GRO2357A6_S5_L001_R1_001.fastq.gz Uninjured-7DPI-3_GRO2357A6_S5_L001_R2_001.fastq.gz,fastq fastq,63524967830.0,538347185.0,GSM8691398 r1,0:28 1:90,A:18434935191;C:13740021920;G:14509703351;T:16838781338;N:1526030,28,90,,,18434935191,13740021920,14509703351,16838781338,1526030,SRX27130830,SRS23587817,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34466,SRR31769118,SRX27130829,SRS23587816,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #2,GSM8691397,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #2,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7,GSM8691397,GSM8691397: adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #2; Danio rerio; RNA Seq,GSM8691397 r1,GSM8691397,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Uninjured-7DPI-2_GRO2559A7_S11_L001_R1_001.fastq.gz Uninjured-7DPI-2_GRO2559A7_S11_L001_R2_001.fastq.gz,fastq fastq,117155938094.0,992846933.0,GSM8691397 r1,0:28 1:90,A:33056566549;C:26122865037;G:28068647978;T:29904980565;N:2877965,28,90,,,33056566549,26122865037,28068647978,29904980565,2877965,SRX27130829,SRS23587816,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34467,SRR31769119,SRX27130828,SRS23587815,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #1,GSM8691396,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #1,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7,GSM8691396,GSM8691396: adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #1; Danio rerio; RNA Seq,GSM8691396 r1,GSM8691396,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Uninjured-7DPI-1_GRO2559A5_S3_L001_R1_001.fastq.gz Uninjured-7DPI-1_GRO2559A5_S3_L001_R2_001.fastq.gz,fastq fastq,88479846662.0,749829209.0,GSM8691396 r1,0:28 1:90,A:24973204142;C:19680603454;G:21127682533;T:22696187157;N:2169376,28,90,,,24973204142,19680603454,21127682533,22696187157,2169376,SRX27130828,SRS23587815,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34468,SRR31769120,SRX27130827,SRS23587814,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #3,GSM8691395,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #3,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691395,GSM8691395: adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #3; Danio rerio; RNA Seq,GSM8691395 r1,GSM8691395,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Injured-7DPI-3_GRO2357A5_S9_L001_R1_001.fastq.gz Injured-7DPI-3_GRO2357A5_S9_L001_R2_001.fastq.gz,fastq fastq,52866571338.0,448021791.0,GSM8691395 r1,0:28 1:90,A:15008347140;C:11559305260;G:12319521011;T:13978097023;N:1300904,28,90,,,15008347140,11559305260,12319521011,13978097023,1300904,SRX27130827,SRS23587814,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34469,SRR31769121,SRX27130826,SRS23587813,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #2,GSM8691394,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #2,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691394,GSM8691394: adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #2; Danio rerio; RNA Seq,GSM8691394 r1,GSM8691394,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Injured-7DPI-2_GRO2559A8_S13_L001_R1_001.fastq.gz Injured-7DPI-2_GRO2559A8_S13_L001_R2_001.fastq.gz,fastq fastq,122844941704.0,1041058828.0,GSM8691394 r1,0:28 1:90,A:34628566594;C:27526793155;G:30025691872;T:30660901278;N:2988805,28,90,,,34628566594,27526793155,30025691872,30660901278,2988805,SRX27130826,SRS23587813,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34470,SRR31769122,SRX27130825,SRS23587812,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #1,GSM8691393,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #1,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691393,GSM8691393: adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #1; Danio rerio; RNA Seq,GSM8691393 r1,GSM8691393,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Injured-7DPI-1_GRO2559A6_S7_L001_R1_001.fastq.gz Injured-7DPI-1_GRO2559A6_S7_L001_R2_001.fastq.gz,fastq fastq,120896581754.0,1024547303.0,GSM8691393 r1,0:28 1:90,A:33711894389;C:26892614943;G:28832438626;T:31456652089;N:2981707,28,90,,,33711894389,26892614943,28832438626,31456652089,2981707,SRX27130825,SRS23587812,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34471,SRR31769123,SRX27130824,SRS23587811,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #3,GSM8691392,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #3,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1,GSM8691392,GSM8691392: adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #3; Danio rerio; RNA Seq,GSM8691392 r1,GSM8691392,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Uninjured-1DPI-3_GRO2657A19_S4_L001_R1_001.fastq.gz Uninjured-1DPI-3_GRO2657A19_S4_L001_R2_001.fastq.gz,fastq fastq,59387016872.0,503279804.0,GSM8691392 r1,0:28 1:90,A:17711412598;C:12536566614;G:13563786736;T:15573793585;N:1457339,28,90,,,17711412598,12536566614,13563786736,15573793585,1457339,SRX27130824,SRS23587811,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34472,SRR31769124,SRX27130823,SRS23587810,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #2,GSM8691391,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #2,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1,GSM8691391,GSM8691391: adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #2; Danio rerio; RNA Seq,GSM8691391 r1,GSM8691391,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Uninjured-1DPI-2_GRO2553A7_S10_L001_R1_001.fastq.gz Uninjured-1DPI-2_GRO2553A7_S10_L001_R2_001.fastq.gz,fastq fastq,106157704906.0,899641567.0,GSM8691391 r1,0:28 1:90,A:29822848120;C:23694191955;G:25190535492;T:27447524885;N:2604454,28,90,,,29822848120,23694191955,25190535492,27447524885,2604454,SRX27130823,SRS23587810,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34473,SRR31769125,SRX27130822,SRS23587809,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #1,GSM8691390,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #1,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1,GSM8691390,GSM8691390: adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #1; Danio rerio; RNA Seq,GSM8691390 r1,GSM8691390,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Uninjured-1DPI-1_GRO2553A5_S2_L001_R1_001.fastq.gz Uninjured-1DPI-1_GRO2553A5_S2_L001_R2_001.fastq.gz,fastq fastq,123090850164.0,1043142798.0,GSM8691390 r1,0:28 1:90,A:34510432265;C:27448485343;G:28965763692;T:32163144642;N:3024222,28,90,,,34510432265,27448485343,28965763692,32163144642,3024222,SRX27130822,SRS23587809,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34474,SRR31769126,SRX27130821,SRS23587808,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #4,GSM8691389,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #4,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691389,GSM8691389: adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #4; Danio rerio; RNA Seq,GSM8691389 r1,GSM8691389,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Injured-1DPI-4_GRO2657A20_S8_L001_R1_001.fastq.gz Injured-1DPI-4_GRO2657A20_S8_L001_R2_001.fastq.gz,fastq fastq,72232326244.0,612138358.0,GSM8691389 r1,0:28 1:90,A:20998820884;C:15527703707;G:16387036598;T:19316988726;N:1776329,28,90,,,20998820884,15527703707,16387036598,19316988726,1776329,SRX27130821,SRS23587808,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34475,SRR31769127,SRX27130820,SRS23587807,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #3,GSM8691388,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #3,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691388,GSM8691388: adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #3; Danio rerio; RNA Seq,GSM8691388 r1,GSM8691388,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Injured-1DPI-3_GRO2357A4_S1_L001_R1_001.fastq.gz Injured-1DPI-3_GRO2357A4_S1_L001_R2_001.fastq.gz,fastq fastq,72891590238.0,617725341.0,GSM8691388 r1,0:28 1:90,A:20358858846;C:16164883435;G:16927165785;T:19438889715;N:1792457,28,90,,,20358858846,16164883435,16927165785,19438889715,1792457,SRX27130820,SRS23587807,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34476,SRR31769128,SRX27130819,SRS23587806,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #2,GSM8691387,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #2,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691387,GSM8691387: adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #2; Danio rerio; RNA Seq,GSM8691387 r1,GSM8691387,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Injured-1DPI-2_GRO2553A8_S12_L001_R1_001.fastq.gz Injured-1DPI-2_GRO2553A8_S12_L001_R2_001.fastq.gz,fastq fastq,91792694538.0,777904191.0,GSM8691387 r1,0:28 1:90,A:25675360853;C:20502226198;G:22024452743;T:23588401816;N:2252928,28,90,,,25675360853,20502226198,22024452743,23588401816,2252928,SRX27130819,SRS23587806,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34477,SRR31769129,SRX27130818,SRS23587805,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #1,GSM8691386,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #1,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691386,GSM8691386: adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #1; Danio rerio; RNA Seq,GSM8691386 r1,GSM8691386,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Injured-1DPI-1_GRO2553A6_S6_L001_R1_001.fastq.gz Injured-1DPI-1_GRO2553A6_S6_L001_R2_001.fastq.gz,fastq fastq,82801648902.0,701708889.0,GSM8691386 r1,0:28 1:90,A:22655489308;C:18871676339;G:19992651055;T:21279810265;N:2021935,28,90,,,22655489308,18871676339,19992651055,21279810265,2021935,SRX27130818,SRS23587805,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
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,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,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