{"database": "metadata", "table": "run_metadata", "rows": [[39895, "SRR2239188", "SRX1181666", "SRS1053969", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells]  with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap  given that over 80% of cutaneous fibers are unmyelinated  that they transduce such important modalities as itch  pain  temperature  touch and pressure  and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective  conditional approach. Overall  the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control  2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type 5 hr treatment replicate 2", "GSM1868439", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head", "wild type 5 hr treatment replicate 2", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads  total number of uniquely aligned reads  genes and transcripts detected  ribosomal fraction  known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp  then GO enrichment analysis was performed in ToppGene suite  with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples  4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0  2 or 5 hours were dissected using a small scalpel  with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies  and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen  Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100  and only those samples having a RIN > 8.7 were used. For library construction  1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized  blunt ended  an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head", "GSM1868439", "GSM1868439: wild type 5 hr treatment replicate 2; Danio rerio; RNA Seq", "GSM1868439", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0  2 or 5 hours were dissected using a small scalpel  with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies  and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen  Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100  and only those samples having a RIN > 8.7 were used. For library construction  1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized  blunt ended  an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868439", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_6_withindex_sequence.txt_GCTTAGA.fq.gz", "fastq", 884810450.0, 17696209.0, "GSM1868439 r1", "0:50", "A:244801024;C:196884736;G:189692109;T:253390454;N:42127", 50, null, null, null, 244801024, 196884736, 189692109, 253390454, 42127, "SRX1181666", "SRS1053969", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.89625, null, 0.26571, null, 0.66247, null, 0.52896, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous 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": ["39895"], "units": {}, "query_ms": 10.346295999625}