Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE20572: mRNA profiling of genetically matched ESCs and iPSCs GSE20575: mRNA profiling of iPSCs and derivative NT-ESCs Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Matthias Stadtfeld

PROVIDER: E-GEOD-20576 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells.

Stadtfeld Matthias M Apostolou Effie E Akutsu Hidenori H Fukuda Atsushi A Follett Patricia P Natesan Sridaran S Kono Tomohiro T Shioda Toshi T Hochedlinger Konrad K

Nature 20100425 7295

Induced pluripotent stem cells (iPSCs) have been generated by enforced expression of defined sets of transcription factors in somatic cells. It remains controversial whether iPSCs are molecularly and functionally equivalent to blastocyst-derived embryonic stem (ES) cells. By comparing genetically identical mouse ES cells and iPSCs, we show here that their overall messenger RNA and microRNA expression patterns are indistinguishable with the exception of a few transcripts encoded within the imprin ...[more]

PMID: 20418860

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Project description:In order to identify genes that are activated in differentiating WT ESCs, but are missing in Tal-1-/- and Runx1-/- ESCs, and which might be involved in the generation of definitive hematopoietic progenitors and their specification thereafter, we performed microarray analyses on purified Flk-1+ cells, differentiated from these ESCs for 4, 5, and 6 days M-bM-^@M-^\in vitroM-bM-^@M-^]. Gene-expression profiling of three biological replicates was performed at days 4, 5, and 6 during the differentiation process of WT J1 ESCs (9 samples), and at day 6 during the differentiation process of either Runx1-/- J1 or Tal-1-/- J1 ESCs (3 samples each). Total RNA was extracted using the RNeasy Mini kit (Qiagen). The integrity and amount of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Complementary DNA was synthesized from 3-5 M-NM-<g total RNA, using reagents recommended in the technical manual GeneChip Expression Analysis (Affymetrix, Santa Clara, CA). The in vitro transcription, necessary for the synthesis of biotinylated complementary RNA (cRNA) was performed using the Enzo RNA Transcript Labeling kit (Affymetrix). Fifteen micrograms of fragmented cRNA of each sample were hybridized to nine Mouse Genome 430-2 arrays (Affymetrix). Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix), according to procedure 2 as described in the technical manual. Finally, the arrays were scanned with a GeneChip Scanner 3000 using the GCOS software, both Affymetrix. All relevant GCOS data of quality checked microarrays were analyzed with High Performance Chip Data Analysis (HPCDA, unpublished), using the BioRetis database (www.bioretis-analysis.de), as described and validated previously (55). Used query parameters for database filtering process was described earlier several times (56). For hierarchical cluster analysis, we used the program Genes@Work (57) with gene vectors for normalization and Pearson w/mean for similarity measure. As cluster type, we used center of mass.

Dataset Information

Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells

Publications

Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells.

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