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| Status |
Public on Jul 16, 2014 |
| Title |
TARBP2_CLIP_rep1 |
| Sample type |
SRA |
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| Source name |
MDA-LM2
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-LM2
transient transfection: myc-tagged TARBP2 vector
rep: 1
antibody: anti-myc Tag, clone 4A6 (Millipore, catalog#: 05-724, lot#: JBC1868960)
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| Treatment protocol |
Cells were treated with a tagged TARBP2 vector (Origene) using TransIT reagent (MirusBio) per manufacturer's instructions.
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| Growth protocol |
Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep
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| Extracted molecule |
total RNA |
| Extraction protocol |
48 hours post-transfection, cells were UV cross-linked and prepared as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).
Samples were prepared for sequencing as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
TARBP2 co-immunoprecipitated RNA
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| Data processing |
Library strategy: HITS-CLIP
After linker sequence removal and quality trimming, sequence mapping was performed using Bowtie with default parameters (build hg19).
ChIPseeqer (strand-specific) was then used to identify the TARBP2 CLIP reads (Giannopoulou et al, BMC Bioinformatics 2011, 12:277). Tags between the replicates were then overlapped between the two biological replicates.
TARBP2 binding sites were then used to generate shuffled sequences, based on a 1st order Markov model (built-in ChIPseeqer function), for further comparisons.
Genome_build: hg19
Supplementary_files_format_and_content: .bed file with the identified TARBP2 binding sites along with their shuffled controls
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| Submission date |
Aug 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Hani Goodarzi |
| Organization name |
UCSF
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| Department |
Biochemistry and Biophysics
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| Street address |
600 16th St, GH S312D
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE49648 |
TARBP2 HITS-CLIP |
| GSE49649 |
Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins |
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| Relations |
| BioSample |
SAMN02313867 |
| SRA |
SRX332668 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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