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| Status |
Public on Apr 25, 2022 |
| Title |
RNA-IP, shADAR1 cells |
| Sample type |
SRA |
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| Source name |
IMR90 cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
condition: shADAR1
antibody: Anti-HuR
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| Extracted molecule |
total RNA |
| Extraction protocol |
Anti-HuR RNA-IP was carried out with a Magna RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore, Cat. No. 17-700). Briefly, for each immunoprecipitation, 2 X 10^7 cells were harvested and lysed in 100 ul RIP Lysis Buffer with RNase and protease inhibitors. The lysate was subjected to immunoprecipitation using 5 ug anti-HuR antibody (Millipore, Cat. No. 03-102). The immunoprecipitated RNAs were extracted using phenol : chloroform : isoamyl alcohol (Thermo Fisher, Cat. No. AM9720) followed by quantitative PCR and RNA-seq.
The RNA library was prepared using KAPA RNA HyperPrep kit (Roche, Cat. No. 07962312001).
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Description |
shA.RIP
RNA-IP
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| Data processing |
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: HuR_RIPseq.txt: Processed data file contains the raw counts for each gene.
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| Submission date |
Feb 25, 2022 |
| Last update date |
Apr 25, 2022 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
priyaw@wistar.org
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| Phone |
2154956837
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| Organization name |
The Wistar Institute
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| Department |
Bioinformatics
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| Lab |
Genomics
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| Street address |
3601 Spruce Street
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL30173 |
| Series (1) |
| GSE179423 |
ADAR1 downregulation contributes to p16INK4a upregulation independent of RNA editing during senescence |
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| Relations |
| BioSample |
SAMN26263403 |
| SRA |
SRX14292787 |
| 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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