Journal: Oncotarget

Article Title: RB1 gene inactivation by chromothripsis in human retinoblastoma

doi:

Figure Lengend Snippet: (A) Heat map and (B) Manhattan plot of inferred log2 ratio of copy number for germline (G) and diagnostic (D) DNA samples of 3 out of 94 samples that carry an amplification in OTX2 detected by SNP6.0 array analysis. (C) OTX2 amplification was validated by quantitative real-time PCR. All data was normalized to CTNNA3 with normal diploid copy number. The dashed line is the cutoff for amplification ≥ 10 copies relative to matched normal DNA for that sample.

Article Snippet: Samples were genotyped using Affymetrix SNP 6.0 microarrays according to the manufacturer's instructions.

Techniques: Diagnostic Assay, Amplification, Real-time Polymerase Chain Reaction

Journal: Oncotarget

Article Title: RB1 gene inactivation by chromothripsis in human retinoblastoma

doi:

Figure Lengend Snippet: (A) Inferred log2 ratio normalized signal for germline and diagnostic DNA samples for samples with MYCN gene amplification. (B) One of the samples indicated by an (*) was previously validated to have a MYCN amplification (SJRB001). Validation of MYCN amplification in the remaining 7 samples using quantitative real-time PCR with a cutoff of 10 copies (dashed line). (C) Inferred log2 ratio for tumor and normal samples and loss of heterozygosity (LOH) for the RB1 gene as measured by SNP 6.0 analysis. (D) Table summarizing single nucleotide variations (SNV), loss of heterozygosity (LOH), promoter hypermethylation and insertions/deletions (INDEL) at the RB1 locus. (E) Immunohistochemistry for RB1 in normal retina, SJRB051 with biallelic RB1 loss and SJRB011 with wild type RB1 . Arrows indicate RB1 immunopositive cells in the normal retina and vascular endothelial cells. (F) PCA plot of gene expression array analysis for the RB1 wild type sample (SJRBO11, yellow) and RB1 deficient retinoblastomas (blue). Scale bars in (E): 10μm.

Article Snippet: Samples were genotyped using Affymetrix SNP 6.0 microarrays according to the manufacturer's instructions.

Techniques: Diagnostic Assay, Amplification, Real-time Polymerase Chain Reaction, Immunohistochemistry, Expressing

Journal: PLoS ONE

Article Title: COPS: A Sensitive and Accurate Tool for Detecting Somatic Copy Number Alterations Using Short-Read Sequence Data from Paired Samples

doi: 10.1371/journal.pone.0047812

Figure Lengend Snippet: SCNAs detected by COPS using reads from tumor:normal paired samples were overlapped with SCNAs detected by cnvPartition2.4.4 Illumina plugin in GenomeStudio with Omni 2.5 whole genome SNP microarray.

Article Snippet: In order to detect sensitivity and specificity of boundary detection using the module, we have compared the boundaries resulting from both the sequencing reads with that from the Illumina whole genome SNP genotyping microarray that use the CNVPartition algorithm to detect boundaries.

Techniques: Microarray

Journal: Oncotarget

Article Title: PADI4 has genetic susceptibility to gastric carcinoma and upregulates CXCR2, KRT14 and TNF-α expression levels

doi: 10.18632/oncotarget.11398

Figure Lengend Snippet: Genotyping result of illumina microarray (control n=384)

Article Snippet: We performed a genotyping assay using a custom-designed Illumina 384-SNP VeraCode microarray (Illumina).

Techniques: Microarray

Journal: Immunity

Article Title: Anti-commensal IgG Drives Intestinal Inflammation and Type 17 Immunity in Ulcerative Colitis

doi: 10.1016/j.immuni.2019.02.006

Figure Lengend Snippet:

Article Snippet: Murine primers: Ccl2 (Mm00441242_m1), Csf2 (Mm01290062_m1), Cxcl1 (Mm04207460_m1), Cxcl2 (Mm00436450_m1), Fcer1g (Mm02343757_m1), Fcgr1 (Mm00438874_m1), Fcgr2b (Mm00438875_m1), Fcgr3 (Mm00438882_m1), Fcgr4 (Mm00519988_m1), Gapdh (Mm99999915_g1), Hprt (Mm03024075_m1), Ifng (Mm01168134_m1), Il1b (Mm00434228_m1), Il6 (Mm00446190_m1), Il10 (Mm01288386_m1), Il17a (Mm00439618_m1), Il22 (Mm01226722_g1), Il23a (Mm00518984_m1), Tnf (Mm00443258_m1), and Tnfsf15 (Mm00770031_m1).

Techniques: Virus, Control, Recombinant, Staining, SYBR Green Assay, Protease Inhibitor, Protein Extraction, Enzyme-linked Immunosorbent Assay, Bicinchoninic Acid Protein Assay, Chromatography, Library Quantification, SNP Genotyping Assay, Gene Expression, Microarray, Infection, Software, Transfection, Transferring