Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA308954 | ENA |
REPOSITORIES: ENA
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Project description:Previous studies of congenic lines of C57BL/6J-DBA/2J mice compared to C57BL/6 mice revealed a 0.23 QTL for sensitivity to methamphetamine on chromosome 11, which contains two protein coding genes, Rufy1 and Hnrnph1. Subsequent transcription activator-like effector nucleases (TALENs)-mediated introduction of frameshift deletions in the first coding exon of one copy of Hnrnph1 of C57BL/6J mice, revealed comparable association to phenotype. Analysis of the transcriptome and splicesome between these Hnrnph1 heterozygous knockouts and C57BL/6J mice revealed genome-wide differentially expression and exon usage of more than 1000 genes in either.
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Project description:We looked for parent of origin effects on genome-wide gene expression in a reciprocal cross between C57BL/6J x B6(C)-H2bm12/KhEgJ mice (the latter strain is a knockout of H2-ab1 on a C57BL/6J background). The aim is to find genes whose expression is altered in trans depending on whether the mother or father carried a knockout allele for H2-ab1. In this experiment differential expression of a gene is inferred from a difference in its overall expression levels. We sequenced RNA from 30 F1 mice from the H2-ab1 heterozygous cross. Both heterozygous and wild type F1 animals were sequenced in order to find both parental and parent of origin effects. We measured expression in the lungs (average 6.2 million reads per sample) and hippocampus (6.6 million reads).
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Project description:This SuperSeries is composed of the following subset Series: GSE41706: Expression data from adult (9 month-old) hearts from GRK2 heterozygous C57BL/6J mice and its wild type littermates GSE41807: Expression data from adult (9 month-old) and young (4 month-old) hearts from C57BL/6J mice GSE41808: Expression data from adult (9 month-old) and young (4 month-old) hearts from GRK2 heterozygous C57BL/6J mice. GSE41809: Expression data from young (4 month-old) hearts from GRK2 heterozygous C57BL/6J mice and its wild type littermates Refer to individual Series
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Project description:RNA sequencing of C57BL/6NJ (B6NJ) x C57BL/6J (B6J) - F2 mice
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Project description:We previously utilized interval-specific congenic lines derived from C57BL/6J (B6) and DBA/2J (D2) alleles to fine map a quantitative trait locus (QTL) influencing methamphetamine (MA)- induced locomotor activity. We identified a 0.23 MB critical interval on chromosome 11 containing only two protein coding genes, Rufy1 and Hnrnph1. Notably, Rufy1 contains three missense SNPs and Hnrnph1 contains 1 SNP near the 5â UTR. In an effort to identify the molecular mechanisms that bridge genetic variation with behavior, we conducted transcriptome analysis via mRNA sequencing (RNA-seq) in a B6.D2 congenic line (chr.11: 50-60 Mb) that captures the QTL. There was an overrepresentation of cis-regulated, differentially expressed genes within the congenic interval (4 out of 92 differentially expressed genes; FDR < 0.05) and widespread genomic regulation on all autosomes. For this study, 3mm punches from both striatal hemispheres were collected and pooled from 16 mice (8 controls and 8 B6.D2 congenics), and RNA was extracted and prepared for cDNA library preparation using the Illumina TruSeq (oligo-dT; 50bp single-end reads). Samples 1-16, consisting of alternating B6 and B6.D2 congenics were run in four lanes total, with samples 1-8 run in duplicate across lanes 5 and 6 and samples 9-16 acorss lanes 7 and 8, respectively. Raw samples provided are labeled with the "CB-" prefix, followed by the sample number and the lane that it was run in is described at the tail end as "_L00#" with # being either lane 5, 6, 7 or 8. In this study, all odd samples (e.g. CB-1,3,5 etc.) are C57BL/6J littermate controls, while all even samples are B6.D2 congenics. Note that the lane 7 replicate for Sample CB-13 (CB-13_L007.fastq.gz) was not processed due to technical difficulties with the file.
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