{"database": "metadata", "table": "run_metadata", "rows": [[67902, "SRR17413283", "SRX13584920", "SRS11474968", "SRP353328", "PRJNA793867", "A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish", "GSE192947", "Other", "Using adult zebrafish inner ears as a model for sensorineural regeneration  we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration  we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4  5 and 7 post DT  and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.", null, "pubmed:36212030", null, "Untreated DTR Utricle scRNAseq", "GSM5769446", null, "tissue:Untreated DTR utricle|strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:N1", "Untreated DTR Utricle scRNAseq", "Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics.  Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex  for barcode processing  for single cell gene counts  for single cell accessibility counts  and aggregating files. For bulk ATAC seq  libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV  TBI  and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode  ATAC signal per barcode  and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq  narrowPeak files contain MACS2 called peaks in BED format.", "Untreated DTR utricle", null, "For single cell experiments  non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments  untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq  cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics. For scATAC seq  libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111  10X Genomics. For bulk ATAC seq  libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.", null, "strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:N1", "GSM5769446", "GSM5769446: Untreated DTR Utricle scRNAseq; Danio rerio; RNA Seq", "GSM5769446 r1", "GSM5769446", "1", "For single cell experiments  non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments  untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq  cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics. For scATAC seq  libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111  10X Genomics. For bulk ATAC seq  libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP353328", null, "assembly:danRer11|intentional duplicate", "DTR_U.bam", "10X Genomics bam file", 2486194893.0, 27320823.0, "GSM5769446 r1", "0:91", "A:754059770;C:498471983;G:530934655;T:699780715;N:2947770", 91, null, null, null, 754059770, 498471983, 530934655, 699780715, 2947770, "SRX13584920", "SRS11474968", "SRA1351664", "Shawn Burgess, NHGRI, NIH", "Shawn Burgess, NHGRI, NIH", 1, 0.91702, null, 0.25265, null, 0.81193, null, 0.71391, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-03", "Adult", "Adult", "Embryo Imprecise", "All anatomical structures"]], "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": ["67902"], "units": {}, "query_ms": 7.019579999905545}