{"database": "metadata", "table": "run_metadata", "rows": [[62939, "SRR13447012", "SRX9860248", "SRS8040679", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish  at 5 xxx post injury. Bulk spinal cord tissue at 5  10  and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 3 gp rp rna 1", "GSM5023601", null, "source name:FACS sorted ctgfa:mCherry;gfap:EGFP cells|tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury", "Z 3 gp rp rna 1", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "FACS sorted ctgfa:mCherry;gfap:EGFP cells", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq  animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted  resuspended  and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury", "GSM5023601", "GSM5023601: Z 3 gp rp rna 1; Danio rerio; RNA Seq", "GSM5023601", null, "1", "For FACS seq  animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted  resuspended  and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023601", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_ATAGGCT.fq.gz", "fastq", 1480993150.0, 29619863.0, "GSM5023601 r1", "0:50 1:0", "A:407241408;C:335585510;G:332782981;T:405104683;N:278568", 50, 0, null, null, 407241408, 335585510, 332782981, 405104683, 278568, "SRX9860248", "SRS8040679", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.90012, null, 0.13909, null, 0.75684, null, 0.59867, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "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": ["62939"], "units": {}, "query_ms": 7.640463998541236}