{"database": "metadata", "table": "run_metadata", "rows": [[51230, "SRR8591750", "SRX5391963", "SRS4379793", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "T cells 1", "GSM3612322", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx", "T cells 1", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx", "GSM3612322", "GSM3612322: T cells 1; Danio rerio; RNA Seq", "GSM3612322", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612322", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "T_cells_1_R2.fq.gz T_cells_1_R1.fq.gz", "fastq fastq", 10355072400.0, 34516908.0, "GSM3612322 r1", "0:150 1:150", "A:2939445450;C:2059218859;G:2124006194;T:3229931547;N:2470350", 150, 150, null, null, 2939445450, 2059218859, 2124006194, 3229931547, 2470350, "SRX5391963", "SRS4379793", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.82838, 0.8272, 0.19005, 0.18949, 0.81128, 0.81227, 0.52045, 0.51858, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "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": ["51230"], "units": {}, "query_ms": 10.524782999709714}