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Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs

Matthew B Friedersdorf and Jack D Keene*

Author Affiliations

Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA

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Genome Biology 2014, 15:R2  doi:10.1186/gb-2014-15-1-r2

Published: 7 January 2014

Additional files

Additional file 1:

Is a figure of the mutational profile of bowtie mapped reads.

Format: PDF Size: 25KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Is a figure showing correlations of background and HuR samples.

Format: PDF Size: 95KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Is a figure showing background and HuR binding to full length MALAT1 transcript.

Format: PDF Size: 218KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Is a figure showing background and HuR binding to full length ELAVL1 transcript.

Format: PDF Size: 267KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the AGO2.EF3D library from [64].

Format: GZ Size: 8KB Download file

Open Data

Additional file 6:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the AGO2.EF3D library from [64].

Format: GZ Size: 188KB Download file

Open Data

Additional file 7:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the AGO2.LCL35 library from [64].

Format: GZ Size: 8KB Download file

Open Data

Additional file 8:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the AGO2.LCL35 library from [64].

Format: GZ Size: 306KB Download file

Open Data

Additional file 9:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the AGO2.LCLBAC library from [64].

Format: GZ Size: 86KB Download file

Open Data

Additional file 10:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the AGO2.LCLBAC library from [64].

Format: GZ Size: 770KB Download file

Open Data

Additional file 11:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the AGO2.LCLBACD1 library from [64].

Format: GZ Size: 66KB Download file

Open Data

Additional file 12:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the AGO2.LCLBACD1 library from [64].

Format: GZ Size: 458KB Download file

Open Data

Additional file 13:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the AGO2.BACD3 library from [64].

Format: GZ Size: 4KB Download file

Open Data

Additional file 14:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the AGO2.BACD3 library from [64].

Format: GZ Size: 46KB Download file

Open Data

Additional file 15:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the AGO2.rep1 library from [18].

Format: GZ Size: 9KB Download file

Open Data

Additional file 16:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the AGO2.rep1 library from [18].

Format: GZ Size: 51KB Download file

Open Data

Additional file 17:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the AGO2.rep2 library from [18].

Format: GZ Size: 36KB Download file

Open Data

Additional file 18:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the AGO2.rep2 library from [18].

Format: GZ Size: 301KB Download file

Open Data

Additional file 19:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the ALKBH5.rep1 library from [38].

Format: GZ Size: 26KB Download file

Open Data

Additional file 20:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the ALKBH5.rep1 library from [38].

Format: GZ Size: 513KB Download file

Open Data

Additional file 21:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the ALKBH5.rep2 library from [38].

Format: GZ Size: 112KB Download file

Open Data

Additional file 22:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the ALKBH5.rep2 library from [38].

Format: GZ Size: 563KB Download file

Open Data

Additional file 23:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the C17ORF85.rep1 library from [38].

Format: GZ Size: 11KB Download file

Open Data

Additional file 24:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the C17ORF85.rep1 library from [38].

Format: GZ Size: 92KB Download file

Open Data

Additional file 25:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the C17ORF85.rep2 library from [38].

Format: GZ Size: 26KB Download file

Open Data

Additional file 26:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the C17ORF85.rep2 library from [38].

Format: GZ Size: 181KB Download file

Open Data

Additional file 27:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the C22ORF28.rep1 library from [38].

Format: GZ Size: 88KB Download file

Open Data

Additional file 28:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the C22ORF28.rep1 library from [38].

Format: GZ Size: 2.7MB Download file

Open Data

Additional file 29:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the C22ORF28.rep2 library from [38].

Format: GZ Size: 243KB Download file

Open Data

Additional file 30:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the C22ORF28.rep2 library from [38].

Format: GZ Size: 1.5MB Download file

Open Data

Additional file 31:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the CAPRIN1.rep1 library from [38].

Format: GZ Size: 268KB Download file

Open Data

Additional file 32:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the CAPRIN1.rep1 library from [38].

Format: GZ Size: 865KB Download file

Open Data

Additional file 33:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the CAPRIN1.rep2 library from [38].

Format: GZ Size: 1.3MB Download file

Open Data

Additional file 34:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the CAPRIN1.rep2 library from [38].

Format: GZ Size: 5.9MB Download file

Open Data

Additional file 35:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the FMR1.I304N.iso1 library from [34].

Format: GZ Size: 12.6MB Download file

Open Data

Additional file 36:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the FMR1.I304N.iso7 library from [34].

Format: GZ Size: 15.7MB Download file

Open Data

Additional file 37:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the FMR1.iso1 library from [34].

Format: GZ Size: 3MB Download file

Open Data

Additional file 38:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the FMR.iso1 library from [34].

Format: GZ Size: 19.2MB Download file

Open Data

Additional file 39:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the FMR1.iso7 library from [34].

Format: GZ Size: 1.4MB Download file

Open Data

Additional file 40:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the FMR.iso7 library from [34].

Format: GZ Size: 12MB Download file

Open Data

Additional file 41:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the FXR1 library from [34].

Format: GZ Size: 171KB Download file

Open Data

Additional file 42:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the FXR1 library from [34].

Format: GZ Size: 2.8MB Download file

Open Data

Additional file 43:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the FXR2 library from [34].

Format: GZ Size: 634KB Download file

Open Data

Additional file 44:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the FXR2 library from [34].

Format: GZ Size: 6.8MB Download file

Open Data

Additional file 45:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the IGF2BP2.rep1 library from [18].

Format: GZ Size: 606KB Download file

Open Data

Additional file 46:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the IGF2BP2.rep1 library from [18].

Format: GZ Size: 6.3MB Download file

Open Data

Additional file 47:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the IGF2BP2.rep2 library from [18].

Format: GZ Size: 10KB Download file

Open Data

Additional file 48:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the IGF2BP2.rep2 library from [18].

Format: GZ Size: 487KB Download file

Open Data

Additional file 49:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the IGF2BP2.rep3 library from [18].

Format: GZ Size: 5KB Download file

Open Data

Additional file 50:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the IGF2BP2.rep3 library from [18].

Format: GZ Size: 163KB Download file

Open Data

Additional file 51:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the IGF2BP2.rep4 library from [18].

Format: GZ Size: 3KB Download file

Open Data

Additional file 52:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the IGF2BP2.rep4 library from [18].

Format: GZ Size: 162KB Download file

Open Data

Additional file 53:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the IGF2BP2.rep5 library from [18].

Format: GZ Size: 5KB Download file

Open Data

Additional file 54:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the IGF2BP2.rep5 library from [18].

Format: GZ Size: 72KB Download file

Open Data

Additional file 55:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the HuR.DMEM library from [37].

Format: GZ Size: 243KB Download file

Open Data

Additional file 56:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the HuR.DMEM library from [37].

Format: GZ Size: 5.7MB Download file

Open Data

Additional file 57:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the HuR.SILAC library from [37].

Format: GZ Size: 272KB Download file

Open Data

Additional file 58:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the HuR.SILAC library from [37].

Format: GZ Size: 3.8MB Download file

Open Data

Additional file 59:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the PUM2.rep1 library from [18].

Format: GZ Size: 1KB Download file

Open Data

Additional file 60:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the PUM2.rep1 library from [18].

Format: GZ Size: 29KB Download file

Open Data

Additional file 61:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the PUM2.rep2 library from [18].

Format: GZ Size: 75KB Download file

Open Data

Additional file 62:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the PUM2.rep2 library from [18].

Format: GZ Size: 1MB Download file

Open Data

Additional file 63:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the ZC3H7B.rep1 library from [38].

Format: GZ Size: 2.1MB Download file

Open Data

Additional file 64:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the ZC3H7B.rep1 library from [38].

Format: GZ Size: 12.9MB Download file

Open Data

Additional file 65:

Is a table of re-analyzed PARalyzer output for clusters of at least 5 reads and 2 T-to-C conversions for the ZC3H7B.rep2 library from [38].

Format: GZ Size: 4.2MB Download file

Open Data

Additional file 66:

Is a table of re-analyzed PARalyzer output for groups indicating all sites utilized by PARalyzer for the ZC3H7B.rep3 library from [38].

Format: GZ Size: 18.6MB Download file

Open Data

Additional file 67:

Is a figure showing binding from multiple PAR-CLIP libraries of different RBPs for full length MALAT1 transcript.

Format: PDF Size: 50KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 68:

Contains a table listing details of the libraries used in analysis for Figure 5B, as well as Supplemental Figure legends and Supplemental References.

Format: DOCX Size: 48KB Download file

Open Data

Additional file 69:

Is a figure showing percent overlap of high abundance sites with background sites.

Format: PDF Size: 24KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 70:

Is a figure showing background correction of Caprin1 PAR-CLIP enriches for A-rich motifs versus U-rich motifs.

Format: PDF Size: 21KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 71:

Is a figure showing saturation analysis of PAR-CLIP libraries.

Format: PDF Size: 22KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data