RIP-seq data for CCNT1
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE43170 | GEO | 2012/12/28
SECONDARY ACCESSION(S): PRJNA184836
REPOSITORIES: GEO
Similar Datasets
Project description:To demonstrate RIPSeeker program that is developed for RIP-seq analyses, we generated RIP-seq data corresponding to the protein CCNT1 in HEK293 cell line using standard RIP-seq protocols described in Zhao et al., (2010). We performed two in-house RIP-seq experiments both for CCNT1 in human HEK293 cells. Briefly, we generated tagged CCNT1 using a triple tag system that supports lentiviral stable expression and mammalian affinity purification (MAPLE) Mak et al (2010). The HEK293 cells stably expressing tagged CCNT1 was purified by M2 agarose beads, followed by RNA extraction by Trizol. The library synthesis was carried out according to the RIP-seq protocol described in Zhao et al., (2010) except that one of the two experiments was done with non-strand-specific sequencing.
2012-12-28 | E-GEOD-43170 | biostudies-arrayexpress
Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Scott Tenenbaum mailto:STenenbaum@uamail.albany.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). The RNA binding protein (RBP) associated mRNA sequencing track (RIP-Seq) is produced as part of the Encyclopedia of DNA Elements (ENCODE) Project (http://hgwdev.cse.ucsc.edu/ENCODE/index.html). This track displays transcriptional fragments associated with RBP in cell lines (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=cellType) K562 and GM12878, using Ribonomic profiling via Illumina SBS. In eukaryotic organisms gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns. These tracks show the associated mRNAs that co-precipitate with the targeted RNA-binding proteins using RIP-Seq profiling. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf RBP-mRNA complexes were purified from cells grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell). RNA samples were amplified and converted to cDNA with the Nugen (http://www.nugeninc.com/) Ovation© RNA-Seq System and prepped for sequencing with the Illumina (http://www.illumina.com/) mRNA-Seq protocol. Approximately 30 million single end sequencing reads were obtained for each K562 and GM12878. RIP samples were analyzed for signal that was at or above the 60th percentile and statistically enriched compared to the negative control. Sequences were analyzed using TopHat (http://tophat.cbcb.umd.edu/) (Trapnell et al., 2009) with Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) (Langmead et al., 2009). Peaks were called from the top 40% of TopHat normalized reads, with a max gap, min run of (24:48). Unions of overlapping peak regions from total RNA replicates (RIP-Input) are presented with p-value from a one tailed t-test for average signal from replicates versus 0 (no cut-off was used for totals). Replicate overlap for positive RIP treatment peaks (ELAVL1 and PABPC1) are presented with a p-value from one tailed t-test versus signal for same the region in negative control replicates (T7-tag). RIP peaks were from sequences longer than 120 bp and p-value < .05. For both totals (RIP-input) and RIPs, the peak scores are scaled relative p-values between treatment and control.
2012-06-06 | E-GEOD-35585 | biostudies-arrayexpress
Project description:m6A modification plays vital roles in regulating mRNA lifecycle, thus controlling the biological process of multiple cell types. Here we intended to discover the binding sites of Mettl3 protein on mRNA of NK cells. Total RNAs were isolated from WT splenic NK cells, and subjected to standard RIP protocol. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Illumina Novaseq 6000 sequencer with PE150 model. Mettl3 binding sites were located primarily in the 3’ untranslated regions (UTRs), coding sequences (CDSs) region and near stop codons.
2021-07-20 | GSE173325 | GEO
Project description:To identify the target mRNAs of the m6A reader protein YTHDF2 in mouse hippocampus, we carired out anti YTHDF2 RNA Immunoprecipitation (RIP) followed by RNA-sequencencing. Using EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from P40 wild type mouse hippocampus was pulled down by rabbit polyclonal anti-YTHDF2 (proteintech) and then sequenced on Illumina Novaseq 6000. The filtered reads were aligned to the mouse reference genome (GRCm38) using BWA mem (v 0.7.12).Then the MACS2 (version 2.1.0) peak calling software was used to identify regions of IP enrichment over background, followed by the motif detected by Homer (Heinz et al., 2010). Peak related genes are then confirmed by PeakAnnotator. Different peak analysis was based on the fold enrichment of peaks of different experiments. A peak was determined as different peak when the odds ratio between two groups was more than 2. Using the same method, genes associated with different peaks were identified. Finally, Biological replicates of anti-YTHDF2 RIP-Seq identified 408 mRNAs transcripts. This study provides gene lists which shows mRNA binding with YTHDF2 in mouse hippocampus.
2023-01-19 | GSE171791 | GEO