{"database": "metadata", "table": "run_metadata", "rows": [[55254, "SRR10204636", "SRX6924595", "SRS5455472", "SRP223753", "PRJNA575017", "Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors", "PRJNA575017", "Other", "In humans  optic nerve damage caused by trauma or diseases such as glaucoma can result in permanent visual loss. The permanence of the damage is due to a failure of the human central nervous system CNS to support regenerative nerve growth. In contrast  fish naturally respond to optic nerve injury by re establishing the growth capacity of CNS neurons and eventually recovering visual function. It is well known that the cellular programming regulating nerve growth and guidance in the developing visual system is highly conserved between fish and humans. Once the mature visual circuitry has been established  the cells undergo a shift in programming from one that promotes the wiring of the visual system to one that promotes the transmittal of light information  gathered in the retina  to the brain where it is perceived as an image. Thus  what appears to set fish apart from humans is their ability to reprogram adult retinal neurons for wiring in response to optic nerve injury. The goal of this study was to understand how adult retinal ganglion cells are reprogrammed for axon growth post optic nerve injury. We achieved this goal by coupling temporal analysis of gene expression with the identification of putative regulatory interactions over the full course of optic nerve regeneration in zebrafish. More specifically  we conducted a temporal analysis of gene expression RNA Seq and chromatin accessibility ATAC Seq over the course of optic nerve regeneration in adult zebrafish. We used time points corresponding to different stages of axon regeneration post optic nerve crush: 2 xxx post injury dpi  initial axon growth past the site of injury; 4 dpi  growth across the midline; 7 dpi  target selection; 12 dpi synaptogenesis.", null, null, "Gene expression Danio rerio adult retina  7 days post optic  nerve crush  replicate 1", "Gene expression Danio rerio adult retina  7 days post optic  nerve crush  replicate 1", "Drerio 7dpi retina RNA  1", null, "strain:fgap43:egfp|age:adult 7 month 9 month|sex:mixed|tissue:regenerating adult retina  7 dpi  bio rep 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Gene expression Danio rerio adult retina  7 days post optic  nerve crush  replicate 1", "Drerio UWM RGC 7RNA1", "Drerio UWM RGC 7RNA1", "RNA was extracted and purified from retinas dissected from adult  fish  7 days post optic nerve crush. RNA was extracted from pooled retinas  using the RNeasy Micro kit Qiagen and concentrated using the RNA Clean  & Concentrator kit Zymo.cDNA libraries were generated for each RNA  sample using Tru Seq Stranded Total & mRNA Sample Prep Kits  Illumina  20020595. Each cDNA library was indexed for multiplexing and subsequently  sequenced on four lanes of the Illumina Hiseq2000. Libraries were sequenced  at 50 bp  3040 million paired end reads/sample", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP223753", null, null, "7RNA1_R1.fastq.gz 7RNA1_R2.fastq.gz", "fastq fastq", 7243600482.0, 71015691.0, "7RNA1 R1.fastq.gz", "0:51 1:51", "A:2022470231;C:1565733898;G:1582218874;T:2060984226;N:12193253", 51, 51, null, null, 2022470231, 1565733898, 1582218874, 2060984226, 12193253, "SRX6924595", "SRS5455472", "SRA970049", "University of Wisconsin Milwaukee|Biological Sciences", "University of Wisconsin Milwaukee", 2, 0.92732, 0.93289, 0.20372, 0.20499, 0.71563, 0.71747, 0.62176, 0.61991, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2019-09-30", "Adult", "Adult", "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": ["55254"], "units": {}, "query_ms": 8.559689013054594}