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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
41543 SRR5006026 SRX2337854 SRS1791073 SRP092952 PRJNA352869 The Biotagging toolkit for analysis of specific cell populations in zebrafish reveals gene regulatory logic encoded in the nuclear transcriptome GSE89670 Other Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types as well as robust methods for tissue specific labeling and biochemical profiling of target proteins. By exploiting multiple transgenesis strategies we have developed a tissue specific binary in vivo biotinylation system in zebrafish termed "biotagging" a versatile methodology that uses genetically encoded components to biotinylate target proteins enabling in depth genome wide analyses of their molecular interactions. Using tissue specific transgenic drivers and individual cell compartment effector lines from our "biotagging" toolkit we demonstrate the specificity of our approach at the biochemical cellular and transcriptional levels. By characterizing the in vivo transcriptional landscape of migratory neural crest and myocardial cells in two different cellular compartments ribosomes and nucleus we identify a comprehensive network of protein coding and non coding RNAs and uncover cis regulatory modules and regulatory logic conferring cell specific identity embedded in the complexity of the non coding nuclear transcriptomes. Our study demonstrates that "biotagging" eliminates background inherent to complex embryonic environments and allows analyses of molecular interactions in any cellular context at highest resolution. Overall design: Examination of RNA seq and ATAC seq using in vivo biotinylated nuclei and polysomes.   pubmed:28402863   Sox10 RNASeq Nuclear 16ss 2 GSM2386489   source name:Sox10 RNASeq Nuclear 16ss|strain/background:AB/TU|tissue:neural crest and otic|developmental stage:16ss|assay:RNA seq stranded|cellular comp1nt:nuclear|ribodepleted:ribodepleted|isolation method:InVivoBiotinylatedNuclei|strand:reverse Sox10 RNASeq Nuclear 16ss 2 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 an enhanced Perl script courtesy of Jim Hughes. RNA seq reads were mapped using STAR v.2.4.2a. BAM files incorporating reads belonging to either DNA strand were generated using custom python script. Genome build: danRer7 Zv9 Supplementary files format and content: bigWig files Sox10 RNASeq Nuclear 16ss   Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext® PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.   strain/background:AB/TU|tissue:neural crest and otic|developmental stage:16ss|assay:RNA seq stranded|cellular comp1nt:nuclear|ribodepleted:ribodepleted|isolation method:InVivoBiotinylatedNuclei|strand:reverse GSM2386489 GSM2386489: Sox10 RNASeq Nuclear 16ss 2; Danio rerio; RNA Seq GSM2386489   1 Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext® PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems. GEO Accession:GSM2386489 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP092952     Sox10_RNASeq_Nuclear_16ss_2_R1.fastq.gz Sox10_RNASeq_Nuclear_16ss_2_R2.fastq.gz fastq fastq 4329094914.0 42442107.0 GSM2386489 r1 0:51 1:51 A:1127420464;C:1030244600;G:1040492979;T:1129785099;N:1151772 51 51     1127420464 1030244600 1040492979 1129785099 1151772 SRX2337854 SRS1791073 SRA491940 GEO Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine 2 0.83089 0.83621 0.48453 0.48562 0.6888 0.68878 0.47815 0.47893 51 51 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2016-11-08 Undetermined Embryo Brain Nervous System