Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of prefrontal cortex samples from 11-week old C57BL6/J and DBA/2J mice housed either with a mouse of the same strain or a mouse of the other strain

ABSTRACT: This experiment was carried out to determine whether social genetic effects (also called indirect genetic effects) contribute to variation in gene expression. That is to say, are differences in gene expression attributable to genetic differences in cage mates? The block factor refers to the order of mouse sacrificing within each cage.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Amelie Baud

PROVIDER: E-MTAB-5276 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

RNA-seq of prefrontal cortex samples from 11-week old C57BL6/J and DBA/2J mice housed either with a mouse of the same strain or a mouse of the other strain

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