Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

MRNA composition of IRP1 mRNPs in mouse tissues

ABSTRACT: Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRP1 (iron regulatory protein 1). Reference Sanchez at al., 2007 Nat. Protoc. Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRPs (iron regulatory proteins). In brief, total RNA was extracted from the reported tissue of four to six C57BL6/J mice using Trizol reagent. mRNA from duodenum, liver and spleen were extracted from mice fed with an iron poor diet (<10mg/kg, Altromin Spezialfutter GmbH & Co, Lage, Germany) for 21 days starting from weaning age. mRNAs from bone marrow and brian were extracted from mice (8-10 weeks old) fed with an iron-normal diet. For each tissue, the RNA samples were pooled and the immunoprecipitations were carried out combining 50 M-BM-5g of total RNA with purified recombinant IRP1 produced in E.coli and a rabbit polyclonal anti-IRP1 antibody. A control reaction in which the recombinant IRP1 was omitted was performed in parallel (referred with the word M-bM-^@M-^\controlM-bM-^@M-^] in the title). All the microarray procedures were conducted at the EMBL Genomics Core Facility using standard Affymetrix protocols. In brief, approximately 120ng of immunoprecipitated RNA was used as input to a two-step amplification procedure to generate biotin-labeled RNA fragments for hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 array (Eukaryotic Sample and Array Processing manual 701024 Rev.3). Intensity values for the hybridizations were obtained either using RMA, calculations done in bioconductor (www.bioconductor.org) or MAS5, calculated using Affymetrix GCOS package. MAS5 calculated intensities were further quantile normalized using bioconductor.

ORGANISM(S): Mus musculus

SUBMITTER: Mayka Sanchez

PROVIDER: E-GEOD-17096 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Iron regulatory protein-1 and -2: transcriptome-wide definition of binding mRNAs and shaping of the cellular proteome by iron regulatory proteins.

Sanchez Mayka M Galy Bruno B Schwanhaeusser Bjoern B Blake Jonathon J Bähr-Ivacevic Tomi T Benes Vladimir V Selbach Matthias M Muckenthaler Martina U MU Hentze Matthias W MW

Blood 20110922 22

Iron regulatory proteins (IRPs) 1 and 2 are RNA-binding proteins that control cellular iron metabolism by binding to conserved RNA motifs called iron-responsive elements (IREs). The currently known IRP-binding mRNAs encode proteins involved in iron uptake, storage, and release as well as heme synthesis. To systematically define the IRE/IRP regulatory network on a transcriptome-wide scale, IRP1/IRE and IRP2/IRE messenger ribonucleoprotein complexes were immunoselected, and the mRNA composition wa ...[more]

PMID: 21940823

Publication: 1/2

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Dataset Information

MRNA composition of IRP1 mRNPs in mouse tissues

Publications

Iron regulatory protein-1 and -2: transcriptome-wide definition of binding mRNAs and shaping of the cellular proteome by iron regulatory proteins.

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