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| Status |
Public on Jun 04, 2016 |
| Title |
K Mock rep1 |
| Sample type |
SRA |
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| Source name |
Mock-inefcted HeLa
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| Organism |
Homo sapiens |
| Characteristics |
antibody: hnRNP K
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| Treatment protocol |
Co-Immunoprecipitation performed using antibodies for hnRNP A1, C1/C2, K or nonspecific IgG. Protein A Sepharose used to bind ab.
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| Growth protocol |
HeLa grown to 70-80% confluence, infected for 6 hours with rWT VSV.
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| Extracted molecule |
total RNA |
| Extraction protocol |
cells lysed with RIPA buffer, centrifuged to remove debris. Co-IP performed. Trizol extraction of aqueous, EtOH precipitation.
Ion Total RNA-Seq Kit v2
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Ion Torrent PGM |
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| Description |
Total RNA (post IP)
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| Data processing |
Base calling was performed using native Ion Torrent PGM software
CLCbio Genomics Workbench 8.0 was used for alignment, filtering, and normalization of abundance to RPKM
tab-delimited text files were exported to Excel (reads >50, repeatable, non-rRNA)
.xlxs files imported to GraphPad Prism for representation
Genome_build: hg19, VSV (NC_001560.1)
Supplementary_files_format_and_content: .xlsx files and GraphPad files contain RPKM and raw read counts
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| Submission date |
Jun 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Adam Davidson |
| E-mail(s) |
davias11@wfu.edu
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| Phone |
9196198835
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| Organization name |
Wake Forest University
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| Department |
Chemistry
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| Lab |
Alexander
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| Street address |
1834 Wake Forest Road
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| City |
Winston-Salem |
| State/province |
NC |
| ZIP/Postal code |
27109 |
| Country |
USA |
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| Platform ID |
GPL17301 |
| Series (1) |
| GSE82226 |
Differential RNA Interactions with Heterogeneous Nuclear Ribonucleoproteins During Vesicular Stomatitis Virus Infection |
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| Relations |
| BioSample |
SAMN05201403 |
| SRA |
SRX1818836 |
| 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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