RNA sequencing of 112kb congenic and C57BL/6J (B6) wild-type littermates reveals differential splicing
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PROVIDER: PRJNA592561 | ENA |
REPOSITORIES: ENA
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Project description:The 112kb congenic was identified via routine monitoring of the proximal and distal SNP sites of the heterozygous Line 4a C57Bl/6J (B6J)-DBA/2J (D2J) congenic offspring (PMID: 26658939). The 112kb congenic was identified via routine monitoring of the proximal and distal SNP sites of the heterozygous Line 4a C57Bl/6J (B6)-DBA/2J (D2) congenic offspring (Yazdani et al. 2015). Like the Line4a congenic, the original mouse of interest possessed a D2J SNP site at the proximal end of the D2J interval (rs29383600; mm9 - chr11:50,186,508, mm10 - chr11:50,373,006). To identify the distal D2J boundary of this new congenic, we generated a list of known SNPs within a roughly 55kb interval spanning downstream from the distal end of the originally characterized 206kb “critical interval” harboring Hnrnph1 and Rufy1 (mm9 - chr11:50,295,887-50,352,284, mm10 - chr11:50,482,385-50,538,782). Starting from the upstream portion of the interval, PCR primers were designed to every five SNPs, and 200bp region around each SNP was amplified, run on a 1.5% agarose gel, visualized for band specificity. Single appropriately-sized bands were then excised and gel purified (Promega Wizard SV Gel and PCR Clean-Up System, Cat A9281), and prepared for sanger sequencing (Genewiz). Using the SNP data from the Mouse Genome Project (Sanger Institute) for reference, the sequenced SNPs were deemed as either heterozygous for B6J and D2J SNPs or homozygous/wildtype B6J. The final SNP we identified as D2 was rs29459915 (mm9 - chr11:50,297,762, mm10 - chr11:50,484,260), and the first SNP we identified as B6 was rs254771403 (mm9 - chr11:50,300,250, mm10 - chr11: 50,486,748).
2019-11-30 | GSE141195 | GEO
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 5’ 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.
2015-12-11 | GSE66366 | GEO
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.
2015-12-11 | E-GEOD-66366 | biostudies-arrayexpress
Project description:We have analyzed the differential expression between the obesity model lean congenic B6.C-D7Mit353 (1) and the background C57BL/6J strains, in four different tissues of male mice: Brain, GWAT (Gonadal White Adipose Tissue), liver and muscle (gastrocnemius). From the 32,381 mouse genes covered by the Applied Biosystems AB1700 microarray system, we identified 330 genes passing FDR at 5% and 188 genes passing FDR at 1%, in any one of the four tissues examined. None of the genes that passed FDR testing were in the congenic donor region. 65 genes from the 8 megabases congenic region were assayed; only six genes (Thrsp, Kctd14, Myo7a, Capn5, Dgat2 and Mtap6) passed statistical significance filtering but not FDR filtering. (1) Diament & Warden 2004: PMID 14569280. Keywords: Congenic mice whole genome gene expression survey
2007-12-01 | GSE7431 | GEO
Project description:We identified a congenic mouse with an introgressed region from the A/J donor inbred strain on an inbred C57BL/6J background that showed a reduced locomotor stimulant response to methamphetamine. We conducted microarray analysis of the striatum from drug-naive female and male mice that were 6-9 weeks old. The congenic region is on chromosome 11 and spans approximately 84-96 Mb. There were two groups of mice used in the analysis: B6 control mice versus congenic mice. Congenic mice were collapsed across heterozygous and homozygous genotypes. All mice are on a C57BL/6J background. Congenic mice differ only on chromosome 11 where they contain the introgressed A/J alleles from 84-96 Mb.
2012-01-18 | GSE35139 | GEO
Project description:We identified a congenic mouse with an introgressed region from the A/J donor inbred strain on an inbred C57BL/6J background that showed a reduced locomotor stimulant response to methamphetamine. We conducted microarray analysis of the striatum from drug-naive female and male mice that were 6-9 weeks old. The congenic region is on chromosome 11 and spans approximately 84-96 Mb. There were two groups of mice used in the analysis: B6 control mice versus congenic mice. Congenic mice were collapsed across heterozygous and homozygous genotypes. All mice are on a C57BL/6J background. Congenic mice differ only on chromosome 11 where they contain the introgressed A/J alleles from 84-96 Mb. 14 C57BL/6J wildtype mice and 14 B6.A/J congenic mice (84-96 Mb region from A/J strain) were examined for gene expression differences using striatal tissue (left and right punches pooled). All mice were drug-naïve and were 6-9 weeks old at the time of sacrifice.
2012-01-18 | E-GEOD-35139 | biostudies-arrayexpress
Project description:Proteins from post-nuclear cell lysates from C57BL/6J WT, CD38-deficient and B6.C-H2bm12/KHEg (bm12) recipient mice at 2 weeks after the adoptive transfer of co-isogenic spleen cells were identified using a proteomic approach. The relative abundances of the proteins identified were calculated using emPAIs scores.
2021-10-11 | PXD026947 | Pride
Project description:A C57BL6/J (B6) x CAST/Ei (CAST) strain intercross was used to identify the first mammalian QTL for macronutrient-specific intake (carbohydrate and fat) and for total energy intake. A region on proximal Chromosome 17 revealed two significant QTL that co-localized for increased macronutrient intake-carbohydrate (Mnic1) and total kilocalorie intake (Kcal2), adjusted for body weight. An interval-specific congenic strain, B6.CAST-17, was then developed which verified the QTL. A new sub-congenic strain was developed which retained the linked traits. Important new findings emerged shows that this congenic interval confers an activity phenotype, i.e., mice carrying the differential segment have 20% higher spontaneous physical activity levels compared with the host B6 strain. We hypothesize that this Chromosome 17 QTL is either encoded by a single gene locus that determines both food intake and physical activity, or by two or more genes, each determining a sub-phenotype of energy balance. Microarray analysis of skeletal muscle and hypothalamus in congenic and wild type B6 mice was carried out to identify potential candidate genes for the activity and food intake behavior. Keywords: macronutrient-specific intake, sub-congenic strain
2009-02-12 | GSE10517 | GEO
Project description:Several studies have shown that bone mineral density (BMD), a clinically measurable predictor of osteoporotic fracture, is the sum of genetic and environmental influences. In addition, serum IGF-1 levels have been correlated to both BMD and fracture risk. We previously identified a Quantitative Trait Locus (QTL) for Bone Mineral Density (BMD) on mouse Chromosome (Chr) 6 that overlaps a QTL for serum IGF-1. The B6.C3H-6T (6T) congenic mouse is homozygous for C57BL/6J (B6) alleles across the genome except for a 30 cM region on Chr 6 that is homozygous for C3H/HeJ (C3H) alleles. This mouse was created to study biology behind both the BMD and the serum IGF-1 QTLs and to identify the gene(s) underlying these QTLs. Female 6T mice have lower BMD and lower serum IGF-1 levels at all ages measured. As the liver is the major source of serum IGF-1, we examined differential expression in the livers of fasted female B6 and 6T mice by microarray. Experiment Overall Design: The experimental design of this experiment was a simple two-factor experiment, with three biological replicates of each factor (in this case mouse strain, B6.C3H-6T vs. C57BL/6J).
2007-11-13 | E-GEOD-5959 | biostudies-arrayexpress
Project description:Murine CD3+ T-cells were immunomagnetically purified from the spleens of C57BL/6J mice and were pretreated in vitro for three days in the presence of R848 (5 μg/ml). Gene expression profile of wild type (WT) C57BL/6J TLR7-primed T-cells, was compared to unmanipulated B6 TLR7 null CD3+ Τ-cells. We used Qiagen Toll-like Receptor RT2 Profiler PCR Array kit to quantitate gene expression profiling of the TLR signaling pathway.
2017-04-21 | GSE80573 | GEO