Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression analysis of inositol hexakisphosphate kinase 1 (IP6K1) knockout mouse embryonic fibroblasts

ABSTRACT: To investigate the biological significance of IP6K1 function we compared the gene expression profile of two mouse embryonic fibroblast (MEF) cell lines each derived from Ip6k1+/+ and Ip6k1-/- embryos. Results reveal downregulation of several biological processes upon the loss of IP6K1. Organism : Mus musculus , Agilent Gene Expression Whole Genome Mouse 4x44k (AMADID: 14868). Two biological replicates each of Ip6k1+/+ and Ip6k1-/- MEFs

ORGANISM(S): Mus musculus

SUBMITTER: Rashna Bhandari

PROVIDER: E-GEOD-73612 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Deletion of inositol hexakisphosphate kinase 1 (IP6K1) reduces cell migration and invasion, conferring protection from aerodigestive tract carcinoma in mice.

Jadav Rathan S RS Kumar Dharmika D Buwa Natasha N Ganguli Shubhra S Thampatty Sitalakshmi R SR Balasubramanian Nagaraj N Bhandari Rashna R

Cellular signalling 20160430 8

Inositol hexakisphosphate kinases (IP6Ks), a family of enzymes found in all eukaryotes, are responsible for the synthesis of 5-diphosphoinositol pentakisphosphate (5-IP7) from inositol hexakisphosphate (IP6). Three isoforms of IP6Ks are found in mammals, and gene deletions of each isoform lead to diverse, non-overlapping phenotypes in mice. Previous studies show a facilitatory role for IP6K2 in cell migration and invasion, properties that are essential for the early stages of tumorigenesis. Howe ...[more]

PMID: 27140681

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Project description:Genomic variation is an inherent phenomena observed among members of same species belonging to different geographical locations. In case of P. falciparum, an apicomplexan protozoan parasite, its 22.8 MB nuclear genome is known to display vast genetic diversity in the subtelomeric compartments having but not exclusively variant gene families like var, rifins and stevors and examples in other elements of the genome have recently been documented. Microarrays, relies solely on the genomic sequence information to capture the relevant transcript abundance and needs to consider these variations into account for revealing true transcriptional variation.Here, we describe the designing strategy of a custom P. falciparum 15K array using Agilent platform to study the transcriptome of Indian field isolates for which genome sequence information is limited. Array contains probes representing genome sequence of two distinct geographical isolates (i.e 3D7 and HB3) and subtelomeric var gene sequence of a third isolate (IT4) known to adhere in culture condition. Probes in the array have been selected based on their efficiency to detect transcripts by performing a 244K array experiment representing multiple probes per gene/transcript. Array performance was evaluated and validated using RNA materials from P. falciparum clinical isolates obtained directly from patients with differing clinical conditions due to malaria infection.Due to pre probe screening large percentage (91 %) of the represented transcripts could be detected from Indian P. falciparum isolates. Replicated probes and multiple probes representing the same gene showed perfect correlation between them suggesting good probe performance. Additional transcripts could be detected due to inclusion of unique probes representing HB3 strain transcripts. Variant surface antigen (VSA) transcripts were detected by optimized probes representing the VSA genes of three geographically distinct strains. Plasmodium falciparum isolates were collected from patients (n=13) with differing clinical conditions. The patients exhibited symptoms categorized as uncomplicated (n=6) or complicated malaria (n=7). Criteria for determination of complicated disease were based on World Health Organization year 2000 guidelines. Microarray array based transcriptional profiling was carried out to evaluate the performance of the array.

Dataset Information

Gene expression analysis of inositol hexakisphosphate kinase 1 (IP6K1) knockout mouse embryonic fibroblasts

Publications

Deletion of inositol hexakisphosphate kinase 1 (IP6K1) reduces cell migration and invasion, conferring protection from aerodigestive tract carcinoma in mice.

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