NYU Dataset

RNA Immunoprecipitation Sequencing (RIP-seq) Reveals ORF1p Association with Prostate Cancer

Part of: Fenyo Lab |
UID: 10492
* Corresponding Author
Description

Long interspersed element-1 (LINE-1) is an autonomous retroelement that utilizes copy and paste mechanism to propagate themselves throughout the genome through a process called retrotransposition. The LINE-1 bicistronic mRNA codes for two proteins, ORF1p and ORF2. While LINE-1 transcription is usually repressed in most healthy somatic cells, ORF1p expression has been observed in tumors, including prostate cancer. This study used RNA immunoprecipitation (RIP) and L1EM analysis software to identify ORF1p bound RNA in prostate cancer cells. They observed that ORF1p bound many non-LINE-1 mRNA in all prostate cancer cell lines that were evaluated. The dataset contains raw sequencing reads. The publication also has supplementary data, which includes three tables. The tables contain data about L1EM estimates of locus specific LINE-1 expression for each of the samples, enrichment of genes in ORF1p IP versus input estimated by DESeq2, and primers used in qPCR experiments.

Subject of Study
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Access

Restrictions
Free to All
Instructions
Raw sequencing reads are available from the Sequence Read Archive (SRA) repository.
Access via SRA


Accession #: PRJNA643489

Associated Publications
Data Type
Equipment Used
Illumina NextSeq 500
Stratagene Stratalinker 2400
Software Used
bcl2fastq v2.20
bedtools
BLAST
CIRIquant
DESeq2
featureCounts
L1EM
ORFfinder
R
SAMtools
STAR
Grant Support