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| Status |
Public on Sep 05, 2016 |
| Title |
Pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice. [iCLIP] |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
Purpose: We aimed to identify the targets of the RNA binding protein ZFP36L1 in thymoctes.
Methods: Total naïve thymocytes from control or DCKO mice were treated with UV light to crosslink RNA and proteins, then RNA-protein complexes were pulled down with anti-ZFP36L1. RNA was extracted and used to make cDNS libraries that were then sequenced by MiSeq 150bp single-end read (Sample 1) and HiSeq2500 RapidRun 50bp single-end read (sample 2, 3).
Results: Sample demultiplexing was performed by identification of the 3 known bases of the 7 bases barcode introduced in the 5’ end of the read by the RCLIP primer. The remaining four random bases were used to remove PCR duplicate reads. Reads were trimmed to remove any adaptor sequence and barcodes before mapping reads to genome GRCm38 using Bowtie. After read mapping, the single-nucleotide at position -1 was annotated as unique ZFP36L1 crosslink site. Identification of highly significant ZFP36L1 binding sites was performed using iCount to assign a FDR to each crosslink site.
Conclusions: We identified ZFP36L1 binding sites in 8675 thymocyte mRNAs.
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| Overall design |
Individual nucleotide resolution cross linking immunoprecipitation (iCLIP) of ZFP36L1-bound RNAs in total naive thymocytes from C57BL/6 mice.
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| Contributor(s) |
Vogel KU, Ahlfors H, Turner M |
| Citation(s) |
27566829 |
| Submission date |
Mar 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Turner |
| E-mail(s) |
martin.turner@babraham.ac.uk
|
| Organization name |
Babraham Institute
|
| Department |
Lymphocyte Signalling and Development
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| Lab |
Dr. Martin Turner
|
| Street address |
Babraham Hall
|
| City |
Cambridge |
| ZIP/Postal code |
CB22 3AT |
| Country |
United Kingdom |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL16417 |
Illumina MiSeq (Mus musculus) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE79179 |
Pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice |
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| Relations |
| BioProject |
PRJNA315111 |
| SRA |
SRP071733 |
