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TranscriptomicsRIP-seq data for CCNT1
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 ce...
ORGANISM(S): Homo sapiens 
2012-12-28 | E-GEOD-43170 | biostudies-arrayexpress
TranscriptomicsGenome-wide identification of Polycomb-associated RNAs by RIP-seq
Large-scale analyses have revealed that 60-90% of the mammalian genome is transcriptionally active. Because <2% of sequences have protein-coding potential, why so much cellular energy is expended on RNA synthesis is a major question in the post-genomic era. The hypothesis that RNA may serve as recru...
ORGANISM(S): Mus musculus 
2010-12-22 | E-GEOD-17064 | biostudies-arrayexpress
TranscriptomicsIdentification of beta-catenin-associated RNAs in myeloid leukaemia cells through RIP-seq
Myeloid cell lines (K562 and HEL) were treated overnight with CHIR99021 or a vehicle control (DMSO). CHIR99021 treatment inhibits GSK3B within the destruction complex functioning in Wnt/beta-catenin signalling pathway, thereby preventing beta-catenin degradation and promoting its stabilization. Foll...
ORGANISM(S): Homo sapiens 
2025-04-08 | E-MTAB-14675 | biostudies-arrayexpress
TranscriptomicsIdentification of the miRNA targetome in hippocampal neurons using RIP-seq
We established a neuron-specific Argonaute2:GFP-RNA immunoprecipitation followed by high throughput sequencing (AGO2-RIP-seq) to analyse the regulatory role of miRNAs in mouse hippocampal neurons. Using this technique, we identified more than two thousand miRNA target genes in hippocampal neurons, r...
ORGANISM(S): Mus musculus 
2015-07-31 | E-GEOD-65543 | biostudies-arrayexpress
TranscriptomicsRIP-seq from ENCODE/SUNY Albany
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...
ORGANISM(S): Homo sapiens 
2012-06-06 | E-GEOD-35585 | biostudies-arrayexpress
TranscriptomicsSu(Hw) and Shep RIP-seq in Kc and BG3 cell lines
Su(Hw) and Shep RIP-seq in Kc and BG3 cell lines RIP-seq with multiple antibodies to two proteins in two Drosophila cell lines, at least 2 replicates for each IP and input
ORGANISM(S): Drosophila melanogaster 
2014-07-29 | E-GEOD-55894 | biostudies-arrayexpress
TranscriptomicsHuR (ELAVL1) RIP-chip and knockdown exon array
Integrative regulatory mapping indicates that the RNA-binding protein HuR (ELAVL1) couples pre-mRNA processing and mRNA stability In this dataset, we employed two distinct experiments. 1) HuR RIP-chip to identify mRNA targets of HuR. 2) HuR knockdown to identify mRNAs whose expression are dependent ...
ORGANISM(S): Homo sapiens 
2011-08-18 | E-GEOD-29778 | biostudies-arrayexpress
Transcriptomicsm6A-RIP-seq of Ascl1-induced neurons.
We performed m6A-RIPs in Ascl1-induced neurons (iNeurons) to investigate the neuronal m6A epitranscriptome. Immunoprecipitation was done twice using two different antibodies, acquired from Abcam and Synaptic Systems (SySy), allowing for a more robust detection of m6A modification marks. Additionally...
ORGANISM(S): Mus musculus 
2023-07-12 | E-MTAB-9542 | biostudies-arrayexpress
TranscriptomicsIdentification of KSHV, EBV and cellular miRNA targets in human B-cells using RIP-Chip
RIP-Chip was performed on DG75-eGFP, DG75-10/12, BCBL-1, BL41, BL41 B95.8 and Jijoye using anti-human Ago2 (11A9) antibodies. Anti-BrdU antibodies were used as controls for DG75-eGFP, DG75-10/12 and BCBL-1. Total RNA was used as control for BL41, BL41 B95.8 and Jijoye. Samples were analyzed on Affym...
ORGANISM(S): Homo sapiens 
2011-02-04 | E-GEOD-17180 | biostudies-arrayexpress
TranscriptomicsRIP-Chip of BRAT and PUM from 0-3 hour Drosophila melanogaster embryos
BRAT-associated mRNAs and PUM-associated mRNAs were identified in early Drosophila embryos by RNA co-immunoprecipitation of the endogenous proteins using synthetic antibodies, followed by microarray analysis (RIP-Chip). Nine RNA co-immunoprecipitations were performed. This includes 3 biological repl...
ORGANISM(S): Drosophila melanogaster 
2015-03-28 | E-GEOD-60466 | biostudies-arrayexpress
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