{"database": "metadata", "table": "run_metadata", "rows": [[53519, "SRR9906841", "SRX6657798", "SRS5218259", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahP20R2", "GSM4007827", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2", "zfRNAnmdahP20R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.", "Retina", "For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2", "GSM4007827", "GSM4007827: zfRNAnmdahP20R2; Danio rerio; RNA Seq", "GSM4007827", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF2P_S2_R1_001.fastq.gz THoa-TF2P_S2_R2_001.fastq.gz", "fastq fastq", 10416796950.0, 69445313.0, "GSM4007827 r1", "0:75 1:75", "A:2846027907;C:2324721617;G:2438862539;T:2805866203;N:1318684", 75, 75, null, null, 2846027907, 2324721617, 2438862539, 2805866203, 1318684, "SRX6657798", "SRS5218259", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.89999, 0.92352, 0.30772, 0.32822, 0.74823, 0.75089, 0.5489, 0.55828, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["53519"], "units": {}, "query_ms": 11.263418000453385}