{"database": "metadata", "table": "run_metadata", "rows": [[60909, "SRR12654011", "SRX9135233", "SRS7377187", "SRP282618", "PRJNA663897", "Identification of enhancer elements that direct long range responses to tissue injury", "GSE158079", "Other", "The goal of this study is to unveal the responses of uninjured tissue to distant tissue injury and the structures required for long range responses to tissue injuries. we profiled responses by the brain and kidney in zebrafish to massive injuries of the heart and identified cebpd transcript induction in both tissue. We also identified and demonstrated that a 1.2kb cebpd downstream element is capable and neccessary for the induction of cebpd in the brain post cardiac injury. Overall design: Brain and kidney RNA seq and ATAC seq profiling post cardiac injury; cebpd+/+ and  cebpd / brain RNA seq profiling post cardiac injury", null, "pubmed:35513710", null, "WKM RNAseq uninjured rep1", "GSM4790350", null, "source name:Whole kidney marrow|strain:EK|tissue:Whole kidney marrow|genotype:Wild type|treatment:uninjured", "WKM RNAseq uninjured rep1", "RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph", "Whole kidney marrow", "animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction and nuclei isolation.", "Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424  Sigma Aldrich and treated with DNase1 to degrade genomic DNA.  Samples were purified with Quick RNA Miniprep kit R1054  Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al.  2013.", "Embryos are raised in 28\u2103 egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.", "strain:EK|tissue:Whole kidney marrow|genotype:Wild type|treatment:uninjured", "GSM4790350", "GSM4790350: WKM RNAseq uninjured rep1; Danio rerio; RNA Seq", "GSM4790350", null, "1", "Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424  Sigma Aldrich and treated with DNase1 to degrade genomic DNA.  Samples were purified with Quick RNA Miniprep kit R1054  Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al.  2013.", "GEO Accession:GSM4790350", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP282618", null, null, "WKM.RNAseq.Uninjured.S4_S16_L007_R1_001.fastq.gz", "fastq", 2227157658.0, 43669758.0, "GSM4790350 r1", "0:51 1:0", "A:537108530;C:560518473;G:511205641;T:618080406;N:244608", 51, 0, null, null, 537108530, 560518473, 511205641, 618080406, 244608, "SRX9135233", "SRS7377187", "SRA1126400", "GEO", "Poss, Cell Biology, Duke University", 1, 0.92052, null, 0.16555, null, 0.72206, null, 0.54742, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-09-16", "Larval", "Larval", "Kidney", "Renal 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": ["60909"], "units": {}, "query_ms": 8.361237007193267}