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 | Controlled By | anatomical_term | Treatment | Hours Post Fertilization | Mutation Description |
---|---|---|---|---|---|---|---|---|---|---|
DCD006414BS | DCD000177SR | tissue | Sauka-Spengler Lab, University of Oxford | AB/TU | 14-19 somites | embryonic structure | — | 17 | — |
Applied Assay ID | Biosample Replicate | Assay | Controlled By |
---|---|---|---|
DCD001082AA | DCD012542BR | RNA-seq_Sauka-Spengler_Lab_0027AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|---|
DCD000875SQ | DCD001087TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2500 | — | ✔ | reverse | 51 | 12/01/2014 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001081AA | DCD012546BR | RNA-seq_Sauka-Spengler_Lab_0027AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|
DCD000874SQ | DCD001081TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2500 | ✔ | reverse | 51 | 12/01/2014 |
Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
---|---|---|---|---|---|---|---|
DCD006416BS | DCD000177SR | tissue | Sauka-Spengler Lab, University of Oxford | AB/TU | 14-19 somites | neural crest | 17 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001083AA | DCD012538BR | RNA-seq_Sauka-Spengler_Lab_0027AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|
DCD000867SQ | DCD001083TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2500 | ✔ | reverse | 51 | 12/01/2014 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001084AA | DCD012553BR | RNA-seq_Sauka-Spengler_Lab_0027AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|
DCD000868SQ | DCD001088TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2500 | ✔ | reverse | 51 | 12/01/2014 |
Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
---|---|---|---|---|---|---|---|
DCD006418BS | DCD000177SR | tissue | Sauka-Spengler Lab, University of Oxford | AB/TU | 14-19 somites | embryonic structure | 17 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001086AA | DCD012543BR | RNA-seq_Sauka-Spengler_Lab_0028AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|
DCD000870SQ | DCD001093TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2500 | ✔ | reverse | 51 | 12/01/2014 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001085AA | DCD012548BR | RNA-seq_Sauka-Spengler_Lab_0028AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|
DCD000869SQ | DCD001089TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2500 | ✔ | reverse | 51 | 12/01/2014 |
Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
---|---|---|---|---|---|---|---|
DCD006421BS | DCD000177SR | tissue | Sauka-Spengler Lab, University of Oxford | AB/TU | 14-19 somites | neural crest | 19 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001088AA | DCD012552BR | RNA-seq_Sauka-Spengler_Lab_0028AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|
DCD000872SQ | DCD001085TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2500 | ✔ | reverse | 51 | 12/01/2014 |
Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
---|---|---|---|---|---|---|---|
DCD006422BS | DCD000177SR | tissue | Sauka-Spengler Lab, University of Oxford | AB/TU | 14-19 somites | neural crest | 17 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001087AA | DCD012539BR | RNA-seq_Sauka-Spengler_Lab_0028AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|
DCD000871SQ | DCD001080TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2500 | ✔ | reverse | 51 | 12/01/2014 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001089AA | DCD012549BR | RNA-seq_Sauka-Spengler_Lab_0028AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|
DCD000873SQ | DCD001082TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2500 | ✔ | reverse | 51 | 12/01/2014 |
Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
---|---|---|---|---|---|---|---|
DCD006423BS | DCD000177SR | tissue | Sauka-Spengler Lab, University of Oxford | AB/TU | 14-19 somites | neural crest | 19 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001090AA | DCD012550BR | RNA-seq_Sauka-Spengler_Lab_0026AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|
DCD000884SQ | DCD001078TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2500 | ✔ | reverse | 51 | 12/01/2014 |
Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
---|---|---|---|---|---|---|---|
DCD006424BS | DCD000177SR | tissue | Sauka-Spengler Lab, University of Oxford | AB/TU | Prim-5 | embryonic structure | 26 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001091AA | DCD012537BR | RNA-seq_Sauka-Spengler_Lab_0028AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|
DCD000876SQ | DCD001094TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2500 | ✔ | reverse | 51 | 12/01/2014 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001092AA | DCD012551BR | RNA-seq_Sauka-Spengler_Lab_0028AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|
DCD000877SQ | DCD001091TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2500 | ✔ | reverse | 51 | 12/01/2014 |
Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
---|---|---|---|---|---|---|---|
DCD006426BS | DCD000177SR | tissue | Sauka-Spengler Lab, University of Oxford | AB/TU | Prim-5 | myocardium | 26 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001094AA | DCD012541BR | RNA-seq_Sauka-Spengler_Lab_0028AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|
DCD000879SQ | DCD001092TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2500 | ✔ | reverse | 51 | 12/01/2014 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001093AA | DCD012545BR | RNA-seq_Sauka-Spengler_Lab_0028AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|
DCD000878SQ | DCD001086TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2500 | ✔ | reverse | 51 | 12/01/2014 |
Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
---|---|---|---|---|---|---|---|
DCD006428BS | DCD000177SR | tissue | Sauka-Spengler Lab, University of Oxford | AB/TU | 26+ somites | neural crest | 24 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001095AA | DCD012544BR | RNA-seq_Sauka-Spengler_Lab_0025AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|
DCD000880SQ | DCD001090TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2000 | unstranded | 51 | 01/01/2013 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001096AA | DCD012547BR | RNA-seq_Sauka-Spengler_Lab_0025AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|
DCD000881SQ | DCD001095TR | Sauka-Spengler Lab, University of Oxford | Illumina | HiSeq 2000 | ✘ | unstranded | 51 | 01/01/2013 |
Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
---|---|---|---|---|---|---|---|
DCD006430BS | DCD000177SR | tissue | Sauka-Spengler Lab, University of Oxford | AB/TU | 14-19 somites | neural crest | 17 |
Applied Assay ID | Biosample Replicate | Assay |
---|---|---|
DCD001098AA | DCD012540BR | ATAC-seq_Sauka-Spengler_Lab_0007AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|
DCD000883SQ | DCD001079TR | Sauka-Spengler Lab, University of Oxford | Illumina | NextSeq 500 High-Output | — | 80 | 03/01/2015 |
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 |