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540 rows where devstage_curation = "Adult" and tissue_curation = "Eye"

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experiment.library_selection 7

technology 5

experiment.platform 3

experiment.library_strategy 2

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Eye · 540 ✖

devstage_curation_coarse 1

devstage_curation 1

  • Adult · 540 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
29113 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
34962 34962 SRR32588719 SRX27895232 SRS24266231 SRP568323 PRJNA1232602 Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains PRJNA1232602 Other In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.       Iso Seq RNA from Danio rerio C2 F2 F EYE   strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:eye|BioSampleModel:Model organism or animal                 Iso Seq RNA from eye C2 F2 F EYE C2 F2 F EYE The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     m64467e_240703_141215.skera.flnc.fastq.gz fastq 36628626441.0 15348616.0 m64467e 240703 141215.skera.flnc.fastq.gz 0:2386.44 A:10655476547;C:7616418469;G:7889834035;T:10466897390;N:0 2386       10655476547 7616418469 7889834035 10466897390 0 SRX27895232 SRS24266231 SRA2089085 National Human Genome Research Institute|Translational and Functional Genomics Branch National Human Genome Research Institute National Human Genome Research Institute                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Eye Sensory System
34972 34972 SRR32588729 SRX27895222 SRS24266219 SRP568323 PRJNA1232602 Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains PRJNA1232602 Other In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.       Iso Seq RNA from Danio rerio C2 F2 M EYE   strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:eye|BioSampleModel:Model organism or animal                 Iso Seq RNA from eye C2 F2 M EYE C2 F2 M EYE The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     m84270_240904_172441_s3.skera.flnc.fastq.gz fastq 80921799737.0 39038804.0 m84270 240904 172441 s3.skera.flnc.fastq.gz 0:2072.86 A:23445079372;C:17292916271;G:17758249005;T:22425555089;N:0 2072       23445079372 17292916271 17758249005 22425555089 0 SRX27895222 SRS24266219 SRA2089085 National Human Genome Research Institute|Translational and Functional Genomics Branch National Human Genome Research Institute National Human Genome Research Institute                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Eye Sensory System
38046 38046 SRR1427469 SRX612649 SRS643610 SRP043465 PRJNA253203 Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration GSE58702 Transcriptome Analysis Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs microRNAs miRNAs that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before during and post completion of zebrafish retinal regeneration   pubmed:25220904   28d GSM1417152   source name:Retina|strain:albino alb / |age:adult|genotype:wildtype|tissue:retina 28d Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al. 2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level Retina   Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012   strain:albino alb / |age:adult|genotype:wildtype|tissue:retina GSM1417152 GSM1417152: 28d; Danio rerio; miRNA Seq GSM1417152   1 Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012 GEO Accession:GSM1417152 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer II   SRP043465     28d.fq bam 694299184.0 32089203.0 GSM1417152 r1 0:21.64 1:0 A:174747494;C:132129648;G:193085254;T:194336788;N:0 21 0     174747494 132129648 193085254 194336788 0 SRX612649 SRS643610 SRA171872 GEO Biological Sciences, Vanderbilt University 1 0.93434   0.05272   0.98831   0.56642   23   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2014-06-20 Adult Adult Eye Sensory System

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