Series Summary for DCD000177SR

The Biotagging toolkit for analysis of specific cell populations reveals gene regulatory logic encoded in the nuclear transcriptome

Survey

10.1016/j.celrep.2017.03.045

GSE89670

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 level. 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.

True

vanessachong

May 18, 2016, 12:44 p.m.

Oct. 22, 2018, 9:54 p.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006414BS DCD000177SR tissue Sauka-Spengler Lab, University of Oxford AB/TU 14-19 somites 17
Applied Assay ID Biosample Replicate Assay
DCD001082AA DCD012542BR RNA-seq_Sauka-Spengler_Lab_0027AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000875SQ DCD001087TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2500 51 12/01/2014
DCD000577DT: FASTQ
DCD003249DT: LOG GRCz10/danRer10
DCD003250DT: TSV GRCz10/danRer10
DCD003251DT: BEDGRAPH GRCz10/danRer10
DCD003253DT: BEDGRAPH GRCz10/danRer10
DCD003254DT: BEDGRAPH GRCz10/danRer10
DCD003255DT: PDF GRCz10/danRer10
DCD003256DT: LOG GRCz10/danRer10
DCD003257DT: PDF GRCz10/danRer10
DCD003258DT: LOG GRCz10/danRer10
DCD003259DT: BEDGRAPH GRCz10/danRer10
DCD003263DT: BEDGRAPH GRCz10/danRer10
DCD003299DT: BAM GRCz10/danRer10
DCD008536DT: BIGWIG GRCz10/danRer10
DCD008538DT: BIGWIG GRCz10/danRer10
DCD013534DT: LOG GRCz11/danRer11
DCD013536DT: TSV GRCz11/danRer11
DCD013537DT: TSV GRCz11/danRer11
DCD013539DT: BEDGRAPH GRCz11/danRer11
DCD013540DT: BEDGRAPH GRCz11/danRer11
DCD013541DT: PDF GRCz11/danRer11
DCD013542DT: BIGWIG GRCz11/danRer11
DCD013543DT: BIGWIG GRCz11/danRer11
DCD013544DT: BEDGRAPH GRCz11/danRer11
DCD013545DT: BEDGRAPH GRCz11/danRer11
DCD013546DT: BAM GRCz11/danRer11
DCD013547DT: LOG GRCz11/danRer11
DCD013548DT: LOG GRCz11/danRer11
DCD013549DT: PDF GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001081AA DCD012546BR RNA-seq_Sauka-Spengler_Lab_0027AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000874SQ DCD001081TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2500 51 12/01/2014
DCD000579DT: FASTQ
DCD003670DT: LOG GRCz10/danRer10
DCD003671DT: TSV GRCz10/danRer10
DCD003672DT: BEDGRAPH GRCz10/danRer10
DCD003674DT: BEDGRAPH GRCz10/danRer10
DCD003675DT: BEDGRAPH GRCz10/danRer10
DCD003676DT: BEDGRAPH GRCz10/danRer10
DCD003677DT: PDF GRCz10/danRer10
DCD003678DT: LOG GRCz10/danRer10
DCD003679DT: PDF GRCz10/danRer10
DCD003680DT: LOG GRCz10/danRer10
DCD003688DT: BEDGRAPH GRCz10/danRer10
DCD003732DT: BAM GRCz10/danRer10
DCD008516DT: BIGWIG GRCz10/danRer10
DCD008517DT: BIGWIG GRCz10/danRer10
DCD013521DT: LOG GRCz11/danRer11
DCD013522DT: TSV GRCz11/danRer11
DCD013523DT: TSV GRCz11/danRer11
DCD013524DT: BEDGRAPH GRCz11/danRer11
DCD013526DT: BIGWIG GRCz11/danRer11
DCD013527DT: BEDGRAPH GRCz11/danRer11
DCD013528DT: BEDGRAPH GRCz11/danRer11
DCD013529DT: BEDGRAPH GRCz11/danRer11
DCD013530DT: PDF GRCz11/danRer11
DCD013531DT: BIGWIG GRCz11/danRer11
DCD013532DT: LOG GRCz11/danRer11
DCD013533DT: LOG GRCz11/danRer11
DCD013535DT: PDF GRCz11/danRer11
DCD013538DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006416BS DCD000177SR tissue Sauka-Spengler Lab, University of Oxford AB/TU 14-19 somites 17
Applied Assay ID Biosample Replicate Assay
DCD001083AA DCD012538BR RNA-seq_Sauka-Spengler_Lab_0027AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000867SQ DCD001083TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2500 51 12/01/2014
DCD000583DT: FASTQ
DCD003188DT: LOG GRCz10/danRer10
DCD003189DT: TSV GRCz10/danRer10
DCD003190DT: BEDGRAPH GRCz10/danRer10
DCD003193DT: BEDGRAPH GRCz10/danRer10
DCD003194DT: BEDGRAPH GRCz10/danRer10
DCD003195DT: BEDGRAPH GRCz10/danRer10
DCD003196DT: PDF GRCz10/danRer10
DCD003197DT: LOG GRCz10/danRer10
DCD003198DT: LOG GRCz10/danRer10
DCD003199DT: PDF GRCz10/danRer10
DCD003203DT: BEDGRAPH GRCz10/danRer10
DCD003230DT: BAM GRCz10/danRer10
DCD008548DT: BIGWIG GRCz10/danRer10
DCD008549DT: BIGWIG GRCz10/danRer10
DCD013493DT: LOG GRCz11/danRer11
DCD013494DT: TSV GRCz11/danRer11
DCD013495DT: TSV GRCz11/danRer11
DCD013496DT: BEDGRAPH GRCz11/danRer11
DCD013497DT: BEDGRAPH GRCz11/danRer11
DCD013498DT: BEDGRAPH GRCz11/danRer11
DCD013499DT: BEDGRAPH GRCz11/danRer11
DCD013501DT: BIGWIG GRCz11/danRer11
DCD013502DT: LOG GRCz11/danRer11
DCD013503DT: PDF GRCz11/danRer11
DCD013504DT: PDF GRCz11/danRer11
DCD013505DT: BIGWIG GRCz11/danRer11
DCD013506DT: LOG GRCz11/danRer11
DCD013510DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001084AA DCD012553BR RNA-seq_Sauka-Spengler_Lab_0027AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000868SQ DCD001088TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2500 51 12/01/2014
DCD000581DT: FASTQ
DCD002167DT: LOG GRCz10/danRer10
DCD002168DT: TSV GRCz10/danRer10
DCD002169DT: BEDGRAPH GRCz10/danRer10
DCD002171DT: BEDGRAPH GRCz10/danRer10
DCD002172DT: BEDGRAPH GRCz10/danRer10
DCD002173DT: BEDGRAPH GRCz10/danRer10
DCD002174DT: PDF GRCz10/danRer10
DCD002175DT: LOG GRCz10/danRer10
DCD002176DT: PDF GRCz10/danRer10
DCD002177DT: LOG GRCz10/danRer10
DCD002178DT: BEDGRAPH GRCz10/danRer10
DCD002198DT: BAM GRCz10/danRer10
DCD008537DT: BIGWIG GRCz10/danRer10
DCD008539DT: BIGWIG GRCz10/danRer10
DCD013507DT: LOG GRCz11/danRer11
DCD013508DT: TSV GRCz11/danRer11
DCD013509DT: TSV GRCz11/danRer11
DCD013511DT: BIGWIG GRCz11/danRer11
DCD013512DT: BEDGRAPH GRCz11/danRer11
DCD013513DT: BEDGRAPH GRCz11/danRer11
DCD013514DT: BIGWIG GRCz11/danRer11
DCD013515DT: BEDGRAPH GRCz11/danRer11
DCD013516DT: BEDGRAPH GRCz11/danRer11
DCD013517DT: LOG GRCz11/danRer11
DCD013518DT: PDF GRCz11/danRer11
DCD013519DT: LOG GRCz11/danRer11
DCD013520DT: PDF GRCz11/danRer11
DCD013525DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006418BS DCD000177SR tissue Sauka-Spengler Lab, University of Oxford AB/TU 14-19 somites 17
Applied Assay ID Biosample Replicate Assay
DCD001086AA DCD012543BR RNA-seq_Sauka-Spengler_Lab_0028AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000870SQ DCD001093TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2500 51 12/01/2014
DCD000584DT: FASTQ
DCD003896DT: LOG GRCz10/danRer10
DCD003897DT: TSV GRCz10/danRer10
DCD003898DT: BEDGRAPH GRCz10/danRer10
DCD003901DT: BEDGRAPH GRCz10/danRer10
DCD003902DT: BEDGRAPH GRCz10/danRer10
DCD003903DT: PDF GRCz10/danRer10
DCD003904DT: BEDGRAPH GRCz10/danRer10
DCD003905DT: LOG GRCz10/danRer10
DCD003906DT: PDF GRCz10/danRer10
DCD003907DT: LOG GRCz10/danRer10
DCD003911DT: BEDGRAPH GRCz10/danRer10
DCD003924DT: BAM GRCz10/danRer10
DCD008483DT: BIGWIG GRCz10/danRer10
DCD008484DT: BIGWIG GRCz10/danRer10
DCD013560DT: LOG GRCz11/danRer11
DCD013561DT: TSV GRCz11/danRer11
DCD013563DT: TSV GRCz11/danRer11
DCD013564DT: BEDGRAPH GRCz11/danRer11
DCD013565DT: BEDGRAPH GRCz11/danRer11
DCD013566DT: BAM GRCz11/danRer11
DCD013567DT: BIGWIG GRCz11/danRer11
DCD013568DT: BEDGRAPH GRCz11/danRer11
DCD013569DT: PDF GRCz11/danRer11
DCD013570DT: BIGWIG GRCz11/danRer11
DCD013571DT: LOG GRCz11/danRer11
DCD013572DT: LOG GRCz11/danRer11
DCD013573DT: PDF GRCz11/danRer11
DCD013575DT: BEDGRAPH GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001085AA DCD012548BR RNA-seq_Sauka-Spengler_Lab_0028AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000869SQ DCD001089TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2500 51 12/01/2014
DCD000586DT: FASTQ
DCD003800DT: LOG GRCz10/danRer10
DCD003801DT: TSV GRCz10/danRer10
DCD003802DT: BEDGRAPH GRCz10/danRer10
DCD003803DT: BEDGRAPH GRCz10/danRer10
DCD003806DT: BEDGRAPH GRCz10/danRer10
DCD003807DT: BEDGRAPH GRCz10/danRer10
DCD003808DT: LOG GRCz10/danRer10
DCD003809DT: PDF GRCz10/danRer10
DCD003810DT: LOG GRCz10/danRer10
DCD003811DT: PDF GRCz10/danRer10
DCD003815DT: BEDGRAPH GRCz10/danRer10
DCD003846DT: BAM GRCz10/danRer10
DCD008676DT: BIGWIG GRCz10/danRer10
DCD013550DT: LOG GRCz11/danRer11
DCD013551DT: TSV GRCz11/danRer11
DCD013552DT: TSV GRCz11/danRer11
DCD013553DT: LOG GRCz11/danRer11
DCD013554DT: PDF GRCz11/danRer11
DCD013555DT: BEDGRAPH GRCz11/danRer11
DCD013556DT: BIGWIG GRCz11/danRer11
DCD013557DT: BEDGRAPH GRCz11/danRer11
DCD013558DT: LOG GRCz11/danRer11
DCD013559DT: PDF GRCz11/danRer11
DCD013562DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006421BS DCD000177SR tissue Sauka-Spengler Lab, University of Oxford AB/TU 14-19 somites 19
Applied Assay ID Biosample Replicate Assay
DCD001088AA DCD012552BR RNA-seq_Sauka-Spengler_Lab_0028AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000872SQ DCD001085TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2500 51 12/01/2014
DCD000587DT: FASTQ
DCD004775DT: LOG GRCz10/danRer10
DCD004776DT: TSV GRCz10/danRer10
DCD004777DT: BEDGRAPH GRCz10/danRer10
DCD004778DT: BEDGRAPH GRCz10/danRer10
DCD004779DT: BEDGRAPH GRCz10/danRer10
DCD004780DT: PDF GRCz10/danRer10
DCD004781DT: LOG GRCz10/danRer10
DCD004782DT: PDF GRCz10/danRer10
DCD004783DT: LOG GRCz10/danRer10
DCD004784DT: BEDGRAPH GRCz10/danRer10
DCD004872DT: BEDGRAPH GRCz10/danRer10
DCD004884DT: BAM GRCz10/danRer10
DCD008713DT: BIGWIG GRCz10/danRer10
DCD013584DT: LOG GRCz11/danRer11
DCD013585DT: TSV GRCz11/danRer11
DCD013586DT: TSV GRCz11/danRer11
DCD013589DT: LOG GRCz11/danRer11
DCD013590DT: PDF GRCz11/danRer11
DCD013591DT: BIGWIG GRCz11/danRer11
DCD013592DT: LOG GRCz11/danRer11
DCD013593DT: PDF GRCz11/danRer11
DCD013597DT: BEDGRAPH GRCz11/danRer11
DCD013598DT: BEDGRAPH GRCz11/danRer11
DCD013601DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006422BS DCD000177SR tissue Sauka-Spengler Lab, University of Oxford AB/TU 14-19 somites 17
Applied Assay ID Biosample Replicate Assay
DCD001087AA DCD012539BR RNA-seq_Sauka-Spengler_Lab_0028AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000871SQ DCD001080TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2500 51 12/01/2014
DCD000588DT: FASTQ
DCD001786DT: LOG GRCz10/danRer10
DCD001787DT: TSV GRCz10/danRer10
DCD001788DT: BEDGRAPH GRCz10/danRer10
DCD001789DT: BEDGRAPH GRCz10/danRer10
DCD001790DT: PDF GRCz10/danRer10
DCD001791DT: LOG GRCz10/danRer10
DCD001792DT: BEDGRAPH GRCz10/danRer10
DCD001793DT: PDF GRCz10/danRer10
DCD001794DT: LOG GRCz10/danRer10
DCD001808DT: BEDGRAPH GRCz10/danRer10
DCD001811DT: BEDGRAPH GRCz10/danRer10
DCD001835DT: BAM GRCz10/danRer10
DCD008688DT: BIGWIG GRCz10/danRer10
DCD013574DT: LOG GRCz11/danRer11
DCD013576DT: TSV GRCz11/danRer11
DCD013577DT: TSV GRCz11/danRer11
DCD013578DT: LOG GRCz11/danRer11
DCD013579DT: PDF GRCz11/danRer11
DCD013580DT: BIGWIG GRCz11/danRer11
DCD013581DT: BEDGRAPH GRCz11/danRer11
DCD013582DT: LOG GRCz11/danRer11
DCD013583DT: PDF GRCz11/danRer11
DCD013587DT: BEDGRAPH GRCz11/danRer11
DCD013588DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001089AA DCD012549BR RNA-seq_Sauka-Spengler_Lab_0028AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000873SQ DCD001082TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2500 51 12/01/2014
DCD000589DT: FASTQ
DCD004785DT: LOG GRCz10/danRer10
DCD004786DT: TSV GRCz10/danRer10
DCD004787DT: BEDGRAPH GRCz10/danRer10
DCD004788DT: LOG GRCz10/danRer10
DCD004789DT: LOG GRCz10/danRer10
DCD004790DT: PDF GRCz10/danRer10
DCD004791DT: PDF GRCz10/danRer10
DCD004795DT: BEDGRAPH GRCz10/danRer10
DCD004871DT: BEDGRAPH GRCz10/danRer10
DCD004879DT: BEDGRAPH GRCz10/danRer10
DCD004880DT: BEDGRAPH GRCz10/danRer10
DCD004885DT: BAM GRCz10/danRer10
DCD008724DT: BIGWIG GRCz10/danRer10
DCD013594DT: LOG GRCz11/danRer11
DCD013595DT: TSV GRCz11/danRer11
DCD013596DT: TSV GRCz11/danRer11
DCD013599DT: BIGWIG GRCz11/danRer11
DCD013600DT: BEDGRAPH GRCz11/danRer11
DCD013602DT: BEDGRAPH GRCz11/danRer11
DCD013603DT: LOG GRCz11/danRer11
DCD013604DT: PDF GRCz11/danRer11
DCD013605DT: PDF GRCz11/danRer11
DCD013606DT: LOG GRCz11/danRer11
DCD013616DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006423BS DCD000177SR tissue Sauka-Spengler Lab, University of Oxford AB/TU 14-19 somites 19
Applied Assay ID Biosample Replicate Assay
DCD001090AA DCD012550BR RNA-seq_Sauka-Spengler_Lab_0026AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000884SQ DCD001078TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2500 51 12/01/2014
DCD000560DT: FASTQ
DCD003513DT: LOG GRCz10/danRer10
DCD003514DT: TSV GRCz10/danRer10
DCD003515DT: BEDGRAPH GRCz10/danRer10
DCD003516DT: BEDGRAPH GRCz10/danRer10
DCD003517DT: BEDGRAPH GRCz10/danRer10
DCD003518DT: BEDGRAPH GRCz10/danRer10
DCD003519DT: PDF GRCz10/danRer10
DCD003520DT: BEDGRAPH GRCz10/danRer10
DCD003521DT: LOG GRCz10/danRer10
DCD003522DT: PDF GRCz10/danRer10
DCD003523DT: LOG GRCz10/danRer10
DCD003564DT: BAM GRCz10/danRer10
DCD008546DT: BIGWIG GRCz10/danRer10
DCD008547DT: BIGWIG GRCz10/danRer10
DCD013476DT: LOG GRCz11/danRer11
DCD013477DT: TSV GRCz11/danRer11
DCD013479DT: TSV GRCz11/danRer11
DCD013482DT: BAM GRCz11/danRer11
DCD013483DT: BEDGRAPH GRCz11/danRer11
DCD013484DT: BEDGRAPH GRCz11/danRer11
DCD013485DT: BEDGRAPH GRCz11/danRer11
DCD013486DT: BEDGRAPH GRCz11/danRer11
DCD013487DT: LOG GRCz11/danRer11
DCD013488DT: PDF GRCz11/danRer11
DCD013489DT: PDF GRCz11/danRer11
DCD013490DT: BIGWIG GRCz11/danRer11
DCD013491DT: BIGWIG GRCz11/danRer11
DCD013492DT: LOG GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006424BS DCD000177SR tissue Sauka-Spengler Lab, University of Oxford AB/TU Prim-5 26
Applied Assay ID Biosample Replicate Assay
DCD001091AA DCD012537BR RNA-seq_Sauka-Spengler_Lab_0028AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000876SQ DCD001094TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2500 51 12/01/2014
DCD000565DT: FASTQ
DCD003837DT: LOG GRCz10/danRer10
DCD003838DT: TSV GRCz10/danRer10
DCD003839DT: BEDGRAPH GRCz10/danRer10
DCD003842DT: BEDGRAPH GRCz10/danRer10
DCD003843DT: PDF GRCz10/danRer10
DCD003844DT: BEDGRAPH GRCz10/danRer10
DCD003845DT: LOG GRCz10/danRer10
DCD003847DT: LOG GRCz10/danRer10
DCD003848DT: PDF GRCz10/danRer10
DCD003851DT: BEDGRAPH GRCz10/danRer10
DCD003855DT: BEDGRAPH GRCz10/danRer10
DCD003895DT: BAM GRCz10/danRer10
DCD008490DT: BIGWIG GRCz10/danRer10
DCD008493DT: BIGWIG GRCz10/danRer10
DCD013607DT: LOG GRCz11/danRer11
DCD013608DT: TSV GRCz11/danRer11
DCD013609DT: TSV GRCz11/danRer11
DCD013610DT: BEDGRAPH GRCz11/danRer11
DCD013611DT: BIGWIG GRCz11/danRer11
DCD013612DT: BEDGRAPH GRCz11/danRer11
DCD013613DT: BEDGRAPH GRCz11/danRer11
DCD013614DT: BEDGRAPH GRCz11/danRer11
DCD013615DT: BIGWIG GRCz11/danRer11
DCD013617DT: BAM GRCz11/danRer11
DCD013618DT: LOG GRCz11/danRer11
DCD013620DT: LOG GRCz11/danRer11
DCD013621DT: PDF GRCz11/danRer11
DCD013622DT: PDF GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001092AA DCD012551BR RNA-seq_Sauka-Spengler_Lab_0028AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000877SQ DCD001091TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2500 51 12/01/2014
DCD000563DT: FASTQ
DCD003705DT: LOG GRCz10/danRer10
DCD003706DT: TSV GRCz10/danRer10
DCD003707DT: BEDGRAPH GRCz10/danRer10
DCD003709DT: BEDGRAPH GRCz10/danRer10
DCD003711DT: BEDGRAPH GRCz10/danRer10
DCD003712DT: PDF GRCz10/danRer10
DCD003713DT: BEDGRAPH GRCz10/danRer10
DCD003714DT: LOG GRCz10/danRer10
DCD003715DT: LOG GRCz10/danRer10
DCD003716DT: PDF GRCz10/danRer10
DCD003720DT: BEDGRAPH GRCz10/danRer10
DCD003751DT: BAM GRCz10/danRer10
DCD008486DT: BIGWIG GRCz10/danRer10
DCD008487DT: BIGWIG GRCz10/danRer10
DCD013619DT: LOG GRCz11/danRer11
DCD013623DT: TSV GRCz11/danRer11
DCD013624DT: TSV GRCz11/danRer11
DCD013625DT: BEDGRAPH GRCz11/danRer11
DCD013626DT: BEDGRAPH GRCz11/danRer11
DCD013627DT: BIGWIG GRCz11/danRer11
DCD013628DT: BEDGRAPH GRCz11/danRer11
DCD013629DT: PDF GRCz11/danRer11
DCD013630DT: BEDGRAPH GRCz11/danRer11
DCD013631DT: BIGWIG GRCz11/danRer11
DCD013632DT: LOG GRCz11/danRer11
DCD013633DT: PDF GRCz11/danRer11
DCD013634DT: BAM GRCz11/danRer11
DCD013635DT: LOG GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006426BS DCD000177SR tissue Sauka-Spengler Lab, University of Oxford AB/TU Prim-5 26
Applied Assay ID Biosample Replicate Assay
DCD001094AA DCD012541BR RNA-seq_Sauka-Spengler_Lab_0028AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000879SQ DCD001092TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2500 51 12/01/2014
DCD000567DT: FASTQ
DCD002107DT: LOG GRCz10/danRer10
DCD002109DT: TSV GRCz10/danRer10
DCD002110DT: BEDGRAPH GRCz10/danRer10
DCD002112DT: BEDGRAPH GRCz10/danRer10
DCD002113DT: BEDGRAPH GRCz10/danRer10
DCD002114DT: PDF GRCz10/danRer10
DCD002115DT: BEDGRAPH GRCz10/danRer10
DCD002116DT: LOG GRCz10/danRer10
DCD002117DT: LOG GRCz10/danRer10
DCD002118DT: PDF GRCz10/danRer10
DCD002122DT: BEDGRAPH GRCz10/danRer10
DCD002179DT: BAM GRCz10/danRer10
DCD008526DT: BIGWIG GRCz10/danRer10
DCD008527DT: BIGWIG GRCz10/danRer10
DCD013649DT: LOG GRCz11/danRer11
DCD013650DT: TSV GRCz11/danRer11
DCD013651DT: TSV GRCz11/danRer11
DCD013652DT: BEDGRAPH GRCz11/danRer11
DCD013653DT: BIGWIG GRCz11/danRer11
DCD013654DT: BEDGRAPH GRCz11/danRer11
DCD013655DT: BEDGRAPH GRCz11/danRer11
DCD013656DT: BIGWIG GRCz11/danRer11
DCD013657DT: BEDGRAPH GRCz11/danRer11
DCD013658DT: LOG GRCz11/danRer11
DCD013659DT: LOG GRCz11/danRer11
DCD013660DT: PDF GRCz11/danRer11
DCD013661DT: PDF GRCz11/danRer11
DCD013665DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001093AA DCD012545BR RNA-seq_Sauka-Spengler_Lab_0028AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000878SQ DCD001086TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2500 51 12/01/2014
DCD000569DT: FASTQ
DCD002023DT: LOG GRCz10/danRer10
DCD002025DT: TSV GRCz10/danRer10
DCD002026DT: BEDGRAPH GRCz10/danRer10
DCD002027DT: BEDGRAPH GRCz10/danRer10
DCD002028DT: BEDGRAPH GRCz10/danRer10
DCD002029DT: BEDGRAPH GRCz10/danRer10
DCD002030DT: PDF GRCz10/danRer10
DCD002031DT: LOG GRCz10/danRer10
DCD002032DT: PDF GRCz10/danRer10
DCD002033DT: LOG GRCz10/danRer10
DCD002034DT: BEDGRAPH GRCz10/danRer10
DCD002099DT: BAM GRCz10/danRer10
DCD008578DT: BIGWIG GRCz10/danRer10
DCD008579DT: BIGWIG GRCz10/danRer10
DCD013636DT: LOG GRCz11/danRer11
DCD013637DT: TSV GRCz11/danRer11
DCD013638DT: TSV GRCz11/danRer11
DCD013639DT: BEDGRAPH GRCz11/danRer11
DCD013640DT: BIGWIG GRCz11/danRer11
DCD013641DT: BIGWIG GRCz11/danRer11
DCD013642DT: BEDGRAPH GRCz11/danRer11
DCD013643DT: BEDGRAPH GRCz11/danRer11
DCD013644DT: BEDGRAPH GRCz11/danRer11
DCD013645DT: PDF GRCz11/danRer11
DCD013646DT: LOG GRCz11/danRer11
DCD013647DT: LOG GRCz11/danRer11
DCD013648DT: PDF GRCz11/danRer11
DCD013666DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006428BS DCD000177SR tissue Sauka-Spengler Lab, University of Oxford AB/TU 26+ somites 24
Applied Assay ID Biosample Replicate Assay
DCD001095AA DCD012544BR RNA-seq_Sauka-Spengler_Lab_0025AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000880SQ DCD001090TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2000 51 01/01/2013
DCD000572DT: FASTQ
DCD004077DT: LOG GRCz10/danRer10
DCD004078DT: TSV GRCz10/danRer10
DCD004079DT: BEDGRAPH GRCz10/danRer10
DCD004081DT: BEDGRAPH GRCz10/danRer10
DCD004082DT: BEDGRAPH GRCz10/danRer10
DCD004083DT: BEDGRAPH GRCz10/danRer10
DCD004084DT: PDF GRCz10/danRer10
DCD004085DT: LOG GRCz10/danRer10
DCD004086DT: PDF GRCz10/danRer10
DCD004087DT: LOG GRCz10/danRer10
DCD004089DT: BEDGRAPH GRCz10/danRer10
DCD004119DT: BAM GRCz10/danRer10
DCD008675DT: BIGWIG GRCz10/danRer10
DCD015175DT: LOG GRCz11/danRer11
DCD015176DT: TSV GRCz11/danRer11
DCD015177DT: TSV GRCz11/danRer11
DCD015178DT: BEDGRAPH GRCz11/danRer11
DCD015179DT: BIGWIG GRCz11/danRer11
DCD015181DT: BEDGRAPH GRCz11/danRer11
DCD015182DT: PDF GRCz11/danRer11
DCD015183DT: LOG GRCz11/danRer11
DCD015184DT: PDF GRCz11/danRer11
DCD015185DT: BAM GRCz11/danRer11
DCD015186DT: LOG GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001096AA DCD012547BR RNA-seq_Sauka-Spengler_Lab_0025AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000881SQ DCD001095TR Sauka-Spengler Lab, University of Oxford Illumina HiSeq 2000 51 01/01/2013
DCD000571DT: FASTQ
DCD004761DT: LOG GRCz10/danRer10
DCD004762DT: TSV GRCz10/danRer10
DCD004764DT: BEDGRAPH GRCz10/danRer10
DCD004765DT: BEDGRAPH GRCz10/danRer10
DCD004768DT: PDF GRCz10/danRer10
DCD004769DT: BEDGRAPH GRCz10/danRer10
DCD004770DT: BEDGRAPH GRCz10/danRer10
DCD004771DT: LOG GRCz10/danRer10
DCD004772DT: PDF GRCz10/danRer10
DCD004773DT: LOG GRCz10/danRer10
DCD004774DT: BEDGRAPH GRCz10/danRer10
DCD004883DT: BAM GRCz10/danRer10
DCD008681DT: BIGWIG GRCz10/danRer10
DCD015187DT: LOG GRCz11/danRer11
DCD015188DT: TSV GRCz11/danRer11
DCD015190DT: TSV GRCz11/danRer11
DCD015191DT: BIGWIG GRCz11/danRer11
DCD015192DT: BEDGRAPH GRCz11/danRer11
DCD015193DT: BEDGRAPH GRCz11/danRer11
DCD015194DT: PDF GRCz11/danRer11
DCD015195DT: PDF GRCz11/danRer11
DCD015196DT: LOG GRCz11/danRer11
DCD015197DT: LOG GRCz11/danRer11
DCD015201DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006430BS DCD000177SR tissue Sauka-Spengler Lab, University of Oxford AB/TU 14-19 somites 17
Applied Assay ID Biosample Replicate Assay
DCD001098AA DCD012540BR ATAC-seq_Sauka-Spengler_Lab_0007AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000883SQ DCD001079TR Sauka-Spengler Lab, University of Oxford Illumina NextSeq 500 High-Output 80 03/01/2015
DCD000573DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001097AA DCD012554BR ATAC-seq_Sauka-Spengler_Lab_0007AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD000882SQ DCD001084TR Sauka-Spengler Lab, University of Oxford Illumina NextSeq 500 High-Output 80 03/01/2015
DCD000575DT: FASTQ