{"database": "metadata", "table": "run_metadata", "rows": [[64335, "SRR14551649", "SRX10895133", "SRS8987958", "SRP319894", "PRJNA730034", "Zebrafish Danio rerio Schwann cell  oligodendrocyte lineage  and neuron RNA sequencing", "GSE174486", "Transcriptome Analysis", "RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP  oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp  and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells  foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells  olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons  nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.", null, "pubmed:33975920", null, "OPC 72hpf Sample2", "GSM5315772", null, "tissue:Zebrafish embryo trunk|strain:AB* Tgolig2:dsred; Tgsox10:megfp|age:72 hpf", "OPC 72hpf Sample2", "For data quality control  FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping  we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5\u2032 to 3\u2032 and removes bases only at the 3\u2032 end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20  the 3\u2032 end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations", "Zebrafish embryo trunk", "72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer\u2019s solution with 2.5mM EDTA and rocked for 15 minutes at 4 \u00b0C. The trunk pieces were washed three times with chilled Dulbecco\u2019s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 \u00b0C  1ml 1x Trypsin with 5% EDTA solution was added  and the samples were incubated for 15 more minutes at 28.5 \u00b0C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 \u03bcm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 \u00b1 750 at each stage were used for RNA sequencing.", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells  Tgolig2:dsred;Tgsox10:megfp for OPC  and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf", "strain:AB* Tgolig2:dsred;Tgsox10:megfp|age:72 hpf", "GSM5315772", "GSM5315772: OPC 72hpf Sample2; Danio rerio; RNA Seq", "GSM5315772", null, "1", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "GEO Accession:GSM5315772", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP319894", null, "loader:latf load", "OPC72_Sample2_R1_001.fastq.gz OPC72_Sample2_R2_001.fastq.gz", "fastq fastq", 7703607275.0, 25797864.0, "GSM5315772 r1", "0:149.33 1:149.29", "A:2052466926;C:1756697559;G:1751055673;T:2142874669;N:512448", 149, 149, null, null, 2052466926, 1756697559, 1751055673, 2142874669, 512448, "SRX10895133", "SRS8987958", "SRA1232603", "GEO", "Kucenas Lab, Biology, University of Virginia", 2, 0.78396, 0.7872, 0.15128, 0.15083, 0.80176, 0.8043, 0.47044, 0.47071, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-05-14", "Larval", "Larval", "Trunk", "Surface Structure"]], "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": ["64335"], "units": {}, "query_ms": 12.624057000721223}