{"database": "metadata", "table": "run_metadata", "rows": [[44566, "SRR6268099", "SRX3374267", "SRS2671493", "SRP124607", "PRJNA417594", "From pioneer to repressor: Bimodal foxd3 activity dynamically remodels neural crest regulatory landscape in vivo", "GSE106676", "Other", "The neural crest NC is a transient embryonic stem cell population characterised by its multipotency and broad developmental potential. Here  we perform NC specific transcriptional and epigenomic profiling of foxd3 mutant versus wild type cells in vivo to define the gene regulatory circuits controlling NC specification. Together with global binding analysis obtained by foxd3 biotin ChIP and single cell profiles of foxd3 expressing premigratory NC  our analysis shows that during early steps of NC formation  foxd3 acts globally as a pioneer factor to prime the onset of genes regulating NC specification and migration by re arranging the chromatin landscape  opening cis regulatory elements and reshuffling nucleosomes. Strikingly  foxd3 then gradually switches from an activator to its previously well described role as a transcriptional repressor. Taken together  these results demonstrate that foxd3 acts bimodally in the neural crest as a switch from 'permissive' to 'repressive' nucleosome/chromatin organisation to maintain multipotency and define cell fates. Overall design: Examination of RNA seq  ATAC seq  histone ChIP seq  Biotin ChIP seq in wild type and foxd3 mutant context at epib stages and in neural crest cells; single cell RNA seq", null, "pubmed:30513303;pubmed:33111104", null, "scRNA seq FoxD3 Citrine 60", "GSM2845253", null, "source name:Citrine reporter expressing cells from 5 6ss embryos|strain:Gtfoxd3 citrinect110|tissue:Citrine reporter expressing cells from 5 6ss embryos|developmental stage:5 6ss|assay:scRNA seq|isolation method:FACS", "scRNA seq FoxD3 Citrine 60", "ChIP seq  Biotin ChIP seq  and ATAC seq reads were trimmed for quality using sickle v 1.33 and mapped using bowtie v.1.0.0. Smoothened bigWig files were generated using a enhanced Perl script courtesy of Jim Hughes. RNA seq reads were mapped using STAR v.2.4.2a Genome build: danRer10", "Citrine reporter expressing cells from 5 6ss embryos", null, "FACS sorted cells were washed with PBS and stored at  80C in lysis buffer. RNA was extracted using Ambion RNAqueous Micro Total RNA isolation kit AM1931  checked on Bioanalyser  samples with RIN >7 were used to prepare cDNA using Takara Clontech SmartSeq2 V4 kit 634889. Sequencing libraries were prepared using Illumina Nextera XT library preparation kit FC 131 1024. For scRNA.seq  individual cells were collected by FACS  cDNA was obtained and sequencing libraries as previously described Picelli et al.  2014. Libraries were sequenced using 50 bp single end reads for 96 cells. 4x10E7 dilution of ERCC spike in control was used.", null, "strain:Gtfoxd3 citrinect110|tissue:Citrine reporter expressing cells from 5 6ss embryos|developmental stage:5 6ss|assay:scRNA seq|isolation method:FACS", "GSM2845253", "GSM2845253: scRNA seq FoxD3 Citrine 60; Danio rerio; RNA Seq", "GSM2845253", null, "1", "FACS sorted cells were washed with PBS and stored at  80C in lysis buffer. RNA was extracted using Ambion RNAqueous Micro Total RNA isolation kit AM1931  checked on Bioanalyser  samples with RIN >7 were used to prepare cDNA using Takara Clontech SmartSeq2 V4 kit 634889. Sequencing libraries were prepared using Illumina Nextera XT library preparation kit FC 131 1024. For scRNA.seq  individual cells were collected by FACS  cDNA was obtained and sequencing libraries as previously described Picelli et al.  2014. Libraries were sequenced using 50 bp single end reads for 96 cells. 4x10E7 dilution of ERCC spike in control was used.", "GEO Accession:GSM2845253", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP124607", null, null, "WTCHG_181145_708506_1.fastq.gz", "fastq", 221176137.0, 4336787.0, "GSM2845253 r1", "0:51", "A:60998674;C:49514363;G:49566398;T:61079758;N:16944", 51, null, null, null, 60998674, 49514363, 49566398, 61079758, 16944, "SRX3374267", "SRS2671493", "SRA629218", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 1, 0.89459, null, 0.09386, null, 0.88136, null, 0.53748, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-11-08", "Undetermined", "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": ["44566"], "units": {}, "query_ms": 7.800039995345287}