Journal: PLoS ONE

Article Title: Transcriptome-Wide Identification of Novel Imprinted Genes in Neonatal Mouse Brain

doi: 10.1371/journal.pone.0003839

Figure Lengend Snippet: (A) Allele counts for Perlegen SNP NES08901860, NES08901861, NES08901863 and NES08901864. The blue bars (from left to right) represent the Illumina read counts from the paternal allele in PWD x AKR and AKR x PWD F1s respectively (maternal genotype listed first). The red bars represent the maternal allele Illumina read counts. (B) Sanger sequencing verification for Perlegen SNP NES08901861. We discovered an adjacent SNP position before NES08901861. The target sequence is GCCCT(AC/GA)ATCT. (C), Pyrosequencing verification for Perlegen SNP NES08901861. The target sequence is GCCCT(AC/GA)ATCT.

Article Snippet: To identify the SNP positions in the mouse RefSeq database, we used the SNP genotype and information in the Perlegen mouse SNP database ( http://mouse.perlegen.com ).

Techniques: Sequencing

Journal: PLoS ONE

Article Title: Transcriptome-Wide Identification of Novel Imprinted Genes in Neonatal Mouse Brain

doi: 10.1371/journal.pone.0003839

Figure Lengend Snippet: (A) Allele counts for the 4 new SNPs discovered by assembling the Solexa reads. The blue bars (from left to right) stand for the counts from the paternal allele in PWD x AKR and AKR x PWD F1s respectively. The red bars represent the maternal allele counts. Four novel SNPs were discovered in one Gtl2 transcript (XR_035484), consistent with monoallelic expression from the maternal allele in both reciprocal crosses and confirmed by Pyrosequencing. Another splicing variant of Gtl2 , NM_144513, previously was found by us to be imprinted using a custom Agilent allele-specific microarray (unpublished), with an 1,847-fold difference in probe intensity in PWD x AKR cross and 793-fold in the reciprocal cross. A Perlegen SNP (NES17649478) in NM_144513 but not XR_035484 was verified by Pyrosequencing. We conclude that both XR_035484 and NM_144513 are imprinted in the neonatal brain. (B) Pyrosequencing verification for novel SNP1 in Gtl2 . The target sequence is TGT(A/G)GAGGGA. (C) Pyrosequencing verification for Perlegen SNP NES17649478. The target sequence is GA(A/G)GATAG.

Article Snippet: To identify the SNP positions in the mouse RefSeq database, we used the SNP genotype and information in the Perlegen mouse SNP database ( http://mouse.perlegen.com ).

Techniques: Expressing, Variant Assay, Microarray, Sequencing

Journal: Nature Communications

Article Title: Pangenome dynamics and population structure of the zoonotic pathogen Salmonella enterica serotype Hadar

doi: 10.1038/s41467-025-68026-3

Figure Lengend Snippet: The networks contain 3384 nodes, connected when Jaccard Index (JI) ≥ 0.988. Eighteen groups (JI-groups A-R) are labeled. Legends are left of each network. a National Center for Biotechnology Information (NCBI) SNP (single-nucleotide polymorphism) cluster across JI-groups (obtained from Pathogen Detection Isolate Browser ). b Condensed allele code across JI-groups. Grey nodes indicate genomes with no assigned allele code. c Plasmid taxonomic units (PTUs) across JI-groups. Grey nodes indicate genomes with no known PTU. d Most common antimicrobial resistance (AMR) genes conferring predicted aminoglycoside and tetracycline resistance. Grey nodes indicate genomes without selected AMR genes. e Genomes determined to be REPTDK01 strains according to Centers for Disease Control and Prevention (CDC)-defined core genome multilocus sequencing typing (cgMLST) allele range. Grey nodes indicate genomes not assigned to REPTDK01. f Genomes isolated from different sources.

Article Snippet: Legends are left of each network. a National Center for Biotechnology Information (NCBI) SNP (single-nucleotide polymorphism) cluster across JI-groups (obtained from Pathogen Detection Isolate Browser ). b Condensed allele code across JI-groups.

Techniques: Labeling, Plasmid Preparation, Control, Sequencing, Isolation

Journal: Nature Communications

Article Title: Pangenome dynamics and population structure of the zoonotic pathogen Salmonella enterica serotype Hadar

doi: 10.1038/s41467-025-68026-3

Figure Lengend Snippet: The network contains 3384 nodes, connected when JI ≥ 0.988. Eighteen groups (JI-groups A-R) are labeled, singleton genomes that do not associate with a JI-group are displayed around the outside of the network. Genomes are colored according to JI-group. Counts and percentages of genomes within each JI-group, along with their dominant National Center for Biotechnology (NCBI) SNP (single nucleotide polymorphism) cluster and plasmid taxonomic unit (PTU) profile are included in the table.

Article Snippet: Legends are left of each network. a National Center for Biotechnology Information (NCBI) SNP (single-nucleotide polymorphism) cluster across JI-groups (obtained from Pathogen Detection Isolate Browser ). b Condensed allele code across JI-groups.

Techniques: Labeling, Plasmid Preparation