{"database": "metadata", "table": "run_metadata", "rows": [[39750, "SRR2089833", "SRX1085047", "SRS981147", "SRP060505", "PRJNA289199", "Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors", "GSE70623", "Transcriptome Analysis", "We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 \u00b5m diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.", null, "pubmed:27376691", null, "cFD only replicate 1", "GSM1812023", null, "tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1", "cFD only replicate 1", "Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis", "embryo", "1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 \u03bcm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 \u00b0C until all samples for 5 biological replicates were obtained.", "post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.", "Zebrafish embryos were obtained from natural spawning", "strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1", "GSM1812023", "GSM1812023: cFD only replicate 1; Danio rerio; RNA Seq", "GSM1812023", null, "1", "post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.", "GEO Accession:GSM1812023", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP060505", null, null, "cntrl_1_1.bz2 cntrl_1_2.bz2", "fastq fastq", 4291177304.0, 21243452.0, "GSM1812023 r1", "0:101 1:101", "A:1182202535;C:708780301;G:753724632;T:1641921837;N:4547999", 101, 101, null, null, 1182202535, 708780301, 753724632, 1641921837, 4547999, "SRX1085047", "SRS981147", "SRA276152", "GEO", "James Chen, Chemical and Systems Biology, Stanford University", 2, 0.45088, 0.8425, 0.11253, 0.11641, 0.97835, 0.84778, 0.46728, 0.64503, 101, 101, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2015-07-08", "Gastrula", "Embryo", "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": ["39750"], "units": {}, "query_ms": 11.131086997920647}