Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression profiles of null Pacman/Xrn1 mutant Drosophila L3 wing imaginal discs

ABSTRACT: Two pcm null alleles (pcm14 and pcm15) were sequenced alongside respective wild-type controls (wild-type 1 and wild-type 2). Each genotype was replicated 3 times. Read depth was 12-17 million reads per replicate. Total RNA was prepared from Drosophila L3 larval wing imaginal discs.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Sarah Newbury

PROVIDER: E-MTAB-3789 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

RNA-seq reveals post-transcriptional regulation of Drosophila insulin-like peptide dilp8 and the neuropeptide-like precursor Nplp2 by the exoribonuclease Pacman/XRN1.

Jones Christopher I CI Pashler Amy L AL Towler Benjamin P BP Robinson Sophie R SR Newbury Sarah F SF

Nucleic acids research 20151209 1

Ribonucleases are critically important in many cellular and developmental processes and defects in their expression are associated with human disease. Pacman/XRN1 is a highly conserved cytoplasmic exoribonuclease which degrades RNAs in a 5'-3' direction. In Drosophila, null mutations in pacman result in small imaginal discs, a delay in onset of pupariation and lethality during the early pupal stage. In this paper, we have used RNA-seq in a genome-wide search for mRNAs misregulated in pacman null ...[more]

PMID: 26656493

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Project description:Human ES cells (hESCs) and human induced pluripotent stem cells (hiPSCs) are usually generated and maintained on living feeder cells like mouse embryonic fibroblasts or on a cell-free substrate like Matrigel. For clinical applications, a quality-controlled, xenobiotic-free culture system is required to minimize risks from contaminating animal-derived pathogens and immunogens. We previously reported that the pericellular matrix of decidua-derived mesenchymal cells (PCM-DM) is an ideal human-derived substrate on which to maintain hiPSCs/hESCs. In this study, we examined whether PCM-DM could be used for the generation and long-term stable maintenance of hiPSCs. Decidua-derived mesenchymal cells (DMCs) were reprogrammed by the retroviral transduction of four factors (OCT4, SOX2, KLF4, c-MYC) and cultured on PCM-DM. The established hiPSC clones expressed alkaline phosphatase, hESC-specific genes and cell-surface markers, and differentiated into three germ layers in vitro and in vivo. At over 20 passages, the hiPSCs cultured on PCM-DM held the same cellular properties with genome integrity as those at early passages. Global gene expression analysis showed that the GDF3, FGF4, UTF1, and XIST expression levels varied during culture, and GATA6 was highly expressed under our culture conditions; however, these gene expressions did not affect the cellsM-bM-^@M-^Y pluripotency. PCM-DM can be conveniently prepared from DMCs, which have a high proliferative potential. Our findings indicate that PCM-DM is a versatile and practical human-derived substrate that can be used for the feeder-cell-free generation and long-term stable maintenance of hiPSCs. Keywords: Induced pluripotent stem cells; Extracellular matrix; Decidua; Mesenchymal cells The microarray study was carried out using Affymetrix Human Genome U133 Plus 2.0 gene expression arrays. Total RNA was extracted from cells with RNeasy (Qiagen), and 100ng of total RNA was used to synthesize aRNA using the 3M-bM-^@M-^Y IVT Express Kit, according to the manufacturerM-bM-^@M-^Ys instructions (Affymetrix Inc., Santa Clara, CA). After aRNA purification, 15 M-NM-<g of aRNA was fragmented and hybridized with a pre-equilibrated GeneChip array (Human Genome U133 Plus 2.0 gene expression array, Affymetrix) at 45M-BM-0C for 16 hours. The GeneChip array was then washed, stained, and scanned according to the manufacturerM-bM-^@M-^Ys instructions. The gene expression data were extracted using Affymetrix Expression Console software.

Dataset Information

Gene expression profiles of null Pacman/Xrn1 mutant Drosophila L3 wing imaginal discs

Publications

RNA-seq reveals post-transcriptional regulation of Drosophila insulin-like peptide dilp8 and the neuropeptide-like precursor Nplp2 by the exoribonuclease Pacman/XRN1.

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