Transcriptomics

Dataset Information

120

Anti-SLBP RIPchip data


ABSTRACT: The animal replication-dependent (RD) histone mRNAs are coordinately regulated with chromosome replication. They are the only known cellular mRNAs that are not polyadenylated. Instead, the mature transcripts end in at a conserved stem-loop (SL) structure. This SL structure interacts stably with the stem-loop binding protein (SLBP), which is involved in all aspects of RD-histone mRNA metabolism. We used several genomic methods, including RNA Binding Protein IP followed by microarray analysis (RIP-ChIP) to analyze the RNA binding landscape of SLBP. Reference based design on two color Agilent DNA microarrays. Experimental sample is labeled in Ch1 (Cy3), which are mRNA bound by the SLBP RNA-binding protein. The reference sample is labeled in Ch2 (Cy5) which are the polyribosomal mRNAs from the supernatant that were not bound by anti-SLBP. Controls included no antibody in the IP (which tends to have non-specific background binding to the beads) and pre-incubation of the SLBP with the antibodies antigenic peptide, which blocks antibody binding to the SLBP.

ORGANISM(S): Homo sapiens  

SUBMITTER: Michael L Whitfield   Michael Whitfield  Lionel Brooks 

PROVIDER: E-GEOD-59915 | ArrayExpress | 2015-12-16

SECONDARY ACCESSION(S): GSE59915PRJNA257063

REPOSITORIES: GEO, ArrayExpress

altmetric image

Publications

A multiprotein occupancy map of the mRNP on the 3' end of histone mRNAs.

Brooks Lionel L   Lyons Shawn M SM   Mahoney J Matthew JM   Welch Joshua D JD   Liu Zhongle Z   Marzluff William F WF   Whitfield Michael L ML  

RNA (New York, N.Y.) 20150916 11


The animal replication-dependent (RD) histone mRNAs are coordinately regulated with chromosome replication. The RD-histone mRNAs are the only known cellular mRNAs that are not polyadenylated. Instead, the mature transcripts end in a conserved stem-loop (SL) structure. This SL structure interacts with the stem-loop binding protein (SLBP), which is involved in all aspects of RD-histone mRNA metabolism. We used several genomic methods, including high-throughput sequencing of cross-linked immunoprec  ...[more]

Similar Datasets

2011-07-20 | E-GEOD-26745 | ArrayExpress
2015-04-22 | E-GEOD-65644 | ArrayExpress
2012-12-13 | E-GEOD-39504 | ArrayExpress
2012-05-02 | E-GEOD-35059 | ArrayExpress
2014-05-05 | E-GEOD-48660 | ArrayExpress
2013-10-01 | E-GEOD-51290 | ArrayExpress
2015-07-08 | E-GEOD-65347 | ArrayExpress
2012-04-06 | E-MEXP-3568 | ArrayExpress
2015-12-16 | E-GEOD-62154 | ArrayExpress
2012-10-21 | E-GEOD-40951 | ArrayExpress