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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 09, 2012 |
| Title |
Transcriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting [CLIP-seq data] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
microRNAs (miRNAs) are essential components of gene regulation, but identification of miRNA targets remains a major challenge. Most target prediction and discovery relies on perfect complementarity of the miRNA seed to the 3’ untranslated region (UTR). However, it is unclear to what extent miRNAs target sites without seed matches. Here, we performed a transcriptome-wide identification of the endogenous targets of a single miRNA—miR-155—in a genetically controlled manner. We found that approximately forty percent of miR-155-dependent Argonaute binding occurs at sites without perfect seed matches. The majority of these non-canonical sites feature extensive complementarity to the miRNA seed with one mismatch. These non-canonical sites confer regulation of gene expression albeit less potently than canonical sites. Thus, non-canonical miRNA binding sites are widespread, often contain seed-like motifs, and can regulate gene expression, generating a continuum of targeting and regulation.
Argonaute (AGO) HITS-CLIP Libraries generated from wild type and miR-155 knockout activated T cells.
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| Overall design |
AGO HITS-CLIP libraries were generated from activated wild type and miR-155 knockout T cells with two different 3' linkers. Libraries were generated and sequenced with an 11nt index read that contained both a 5nt multiplexing index and a 6nt degenerate barcode. Files have been demultiplexed and the 6nt degenerate barcode has been appended as the first 6 nucleotides of the read.
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| Contributor(s) |
Loeb GB, Khan AA, Canner D, Hiatt JB, Shendure J, Darnell RB, Leslie CS, Rudensky AY |
| Citation(s) |
23142080 |
| Submission date |
Oct 02, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Aly Azeem Khan |
| Organization name |
University of Chicago
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| Street address |
6045 S. Kenwood Ave.
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platforms (1) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
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| Samples (24)
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| GSM1013578 |
CD4+ T cells, 155KO, biological rep4 |
| GSM1013579 |
CD4+ T cells, 155KO, biological rep5 |
| GSM1013580 |
CD4+ T cells, 155KO, biological rep6 |
| GSM1013581 |
CD4+ T cells, 155KO, biological rep7 |
| GSM1013582 |
CD4+ T cells, 155KO, biological rep8 |
| GSM1013583 |
CD4+ T cells, 155KO, biological rep9 |
| GSM1013584 |
CD4+ T cells, 155KO, biological rep10 |
| GSM1013585 |
CD4+ T cells, 155KO, biological rep11 |
| GSM1013586 |
CD4+ T cells, 155KO, biological rep12 |
| GSM1013587 |
CD4+ T cells, WT, biological rep1 |
| GSM1013588 |
CD4+ T cells, WT, biological rep2 |
| GSM1013589 |
CD4+ T cells, WT, biological rep3 |
| GSM1013590 |
CD4+ T cells, WT, biological rep4 |
| GSM1013591 |
CD4+ T cells, WT, biological rep5 |
| GSM1013592 |
CD4+ T cells, WT, biological rep6 |
| GSM1013593 |
CD4+ T cells, WT, biological rep7 |
| GSM1013594 |
CD4+ T cells, WT, biological rep8 |
| GSM1013595 |
CD4+ T cells, WT, biological rep9 |
| GSM1013596 |
CD4+ T cells, WT, biological rep10 |
| GSM1013597 |
CD4+ T cells, WT, biological rep11 |
| GSM1013598 |
CD4+ T cells, WT, biological rep12 |
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| This SubSeries is part of SuperSeries: |
| GSE41288 |
Transcriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting |
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| Relations |
| BioProject |
PRJNA176456 |
| SRA |
SRP015971 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE41285_clip_peaks.txt.gz |
651.8 Kb |
(ftp)(http) |
TXT |
| GSE41285_clip_supplemental.pdf.gz |
113.2 Kb |
(ftp)(http) |
PDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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