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| Status |
Public on Dec 01, 2013 |
| Title |
Mbnl1-/-, reps 1-3 |
| Sample type |
SRA |
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| Source name |
Quadriceps, Mbnl1-/-
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| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: Mbnl1-/-
age: 15-16 weeks
tissue: quadriceps muscle
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| Extracted molecule |
total RNA |
| Extraction protocol |
Quadriceps muscle was dissected from WT and Mbnl1-/- mice (15-16 weeks of age), snap frozen and powdered in liquid N2 and crosslinked with UV-light using a Stratalinker 1800 (Stratagene). Cell lysates were prepared and protein-RNA complexes were isolated by immunoprecipitation.
Immunoprecipitation was performed using Mbnl2-specific antibody ((Santa Cruz Biotechnology); Catalog number: sc 136167), mAb 3B4 and RNA tags were generated using RNase A concentrations of 38.6 U/ml and 0.0386 U/ml for high and low RNase, respectively. RNA tags bound to Mbnl2 were separated on a SDS gel, isolated, purified, precipitated and converted to cDNA libraries. These libraries were tagged with linkers and Illumina-specific sequencing adapters during the preparation and submitted for sequencing on the Illumina Genome Analyzer IIx.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
Total RNA-Protein Complex
BED files from all the 3 bioreps of Mbnl1-/- were merged to produce one final processed file.
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| Data processing |
Library strategy: HITS-CLIP
Raw reads filtered to remove low quality reads by requiring a minimum score of 20 in 4nt barcode positions and an average score of 20 in the following 25 nucleotides.
The filtered reads were then aligned to the mouse reference genome (UCSC mm9) by BWA.
Potential PCR duplicates, as judged from the starting position of genomic mapping and the barcode sequences, were removed to identify unique CLIP tags.
Genome_build: MGSCv37
Supplementary_files_format_and_content: BED
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| Submission date |
Jun 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Maurice Swanson |
| E-mail(s) |
mswanson@ufl.edu
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| Phone |
3522738076
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| Organization name |
University of Florida
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| Department |
Molecular Genetics and Microbiology
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| Lab |
220G
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| Street address |
2033 Mowry Road
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| City |
Gainesville |
| State/province |
Fl |
| ZIP/Postal code |
32608 |
| Country |
USA |
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| Platform ID |
GPL11002 |
| Series (1) |
| GSE47794 |
Compound loss of muscleblind-like function in myotonic dystrophy |
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| Relations |
| BioSample |
SAMN02194140 |
| SRA |
SRX298279 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1159717_2012-M1KO_Merge.bed.gz |
7.6 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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