Ji et al. 2015 (PRJNA275305)
General Details
| Title | Ribosome profiling and RNA sequencing of MCF10A-ER-Src and fibroblast cell transformation |
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| Organism | |
| Number of Samples | 26 |
| Release Date | 2015/02/12 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP054971 |
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| ENA | SRP054971 |
| GEO | GSE65885 |
| BioProject | PRJNA275305 |
Publication
| Title | |
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| Authors | Ji Z, Song R, Huang H, Regev A, Struhl K |
| Journal | Nature biotechnology |
| Publication Date | 2016 Apr |
| Abstract | Ribosome profiling is widely used to study translation in vivo, but not all sequence reads correspond to ribosome-protected RNA. Here we describe Rfoot, a computational pipeline that analyzes ribosomal profiling data and identifies native, nonribosomal RNA-protein complexes. We use Rfoot to precisely map RNase-protected regions within small nucleolar RNAs, spliceosomal RNAs, microRNAs, tRNAs, long noncoding (lnc)RNAs and 3' untranslated regions of mRNAs in human cells. We show that RNAs of the same class can show differential complex association. Although only a subset of lncRNAs show RNase footprints, many of these have multiple footprints, and the protected regions are evolutionarily conserved, suggestive of biological functions. |
| PMC | PMC4824641 |
| PMID | 26900662 |
| DOI |
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
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| SRR1802129 | PRJNA275305 | Homo sapiens | MCF10A | Ribo-Seq | Cycloheximide |  |
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| SRR1802130 | PRJNA275305 | Homo sapiens | MCF10A | Ribo-Seq | Cycloheximide | |
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| SRR1802131 | PRJNA275305 | Homo sapiens | MCF10A | Ribo-Seq | Cycloheximide | |
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| SRR1802132 | PRJNA275305 | Homo sapiens | MCF10A | Ribo-Seq | Cycloheximide | |
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| SRR1802133 | PRJNA275305 | Homo sapiens | MCF10A | Ribo-Seq | Harringtonine | |
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| SRR1802134 | PRJNA275305 | Homo sapiens | MCF10A | Ribo-Seq | Harringtonine | |
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| SRR1802135 | PRJNA275305 | Homo sapiens | MCF10A | Ribo-Seq | Harringtonine | |
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| SRR1802136 | PRJNA275305 | Homo sapiens | MCF10A | Ribo-Seq | Harringtonine | |
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| SRR1802137 | PRJNA275305 | Homo sapiens | MCF10A | Ribo-Seq | Cycloheximide | |
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| SRR1802138 | PRJNA275305 | Homo sapiens | MCF10A | Ribo-Seq | Cycloheximide | |
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| SRR1802139 | PRJNA275305 | Homo sapiens | MCF10A | Ribo-Seq | Cycloheximide | |
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| SRR1802140 | PRJNA275305 | Homo sapiens | MCF10A | Ribo-Seq | Cycloheximide | |
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| SRR1802141 | PRJNA275305 | Homo sapiens | MCF10A | Ribo-Seq | Cycloheximide | |
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| SRR1802142 | PRJNA275305 | Homo sapiens | MCF10A | Ribo-Seq | Cycloheximide | |
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| SRR1802146 | PRJNA275305 | Homo sapiens | BJ | Ribo-Seq | Cycloheximide | |
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| SRR1802147 | PRJNA275305 | Homo sapiens | BJ | Ribo-Seq | Cycloheximide | |
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| SRR1802148 | PRJNA275305 | Homo sapiens | BJ | Ribo-Seq | Cycloheximide | |
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| SRR1802149 | PRJNA275305 | Homo sapiens | BJ | Ribo-Seq | Harringtonine | |
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| SRR1802150 | PRJNA275305 | Homo sapiens | BJ | Ribo-Seq | Harringtonine | |
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| SRR1802151 | PRJNA275305 | Homo sapiens | BJ | Ribo-Seq | Harringtonine | |
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| SRR1802152 | PRJNA275305 | Homo sapiens | BJ | Ribo-Seq | Cycloheximide | |
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| SRR1802153 | PRJNA275305 | Homo sapiens | BJ | Ribo-Seq | Cycloheximide | |
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| SRR1802154 | PRJNA275305 | Homo sapiens | BJ | Ribo-Seq | Cycloheximide | |
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| SRR1802155 | PRJNA275305 | Homo sapiens | BJ | Ribo-Seq | Harringtonine | |
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| SRR1802156 | PRJNA275305 | Homo sapiens | BJ | Ribo-Seq | Harringtonine | |
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| SRR1802157 | PRJNA275305 | Homo sapiens | BJ | Ribo-Seq | Harringtonine | |
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| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) |
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