raw expression tcga data (.cel files arrays  (Thermo Fisher)

Journal: PLoS ONE

Article Title: Altered Expression of Polycomb Group Genes in Glioblastoma Multiforme

doi: 10.1371/journal.pone.0080970

Figure Lengend Snippet: ( A ) PcG gene expression in TCGA glioblastoma multiforme (GBM) subtypes. Using the TCGA data for GBM, pair-wise comparisons were conducted between all 4 of the molecular subtypes (Mesenchymal, Classical, Neural and Proneural, color coded). ** P<0.01. ( B ) Continuum of abnormal expression in PcG genes in different histological grades of astrocytomas. The Y-axis measures the background adjusted Robust Multi-array Average (RMA) which indicates the normalized expression level. Box-and-whisker plots show the distribution of mRNA expression in normal brain and different grades of astrocytomas (color coded). For detailed statistical analyses, please see & .

Article Snippet: Robust multichip average (RMA) normalization was applied to raw expression TCGA data (.CEL files for Affymetrix arrays) .

Techniques: Expressing, Whisker Assay

Journal: BMC Genomics

Article Title: Genomic expression during human myelopoiesis

doi: 10.1186/1471-2164-8-264

Figure Lengend Snippet: Gene expression dataset . A) The gene expression dataset analyzed comprises cell samples from different levels of myeloid differentiation process (stem/progenitor cells, precursors and terminally differentiated cells). The graph describes relationships between the cellular contexts analyzed within myeloid differentiation tree. For each cell type, the number of samples examined with independent microarray experiments is indicated in brackets. B) Dendrogram obtained by unsupervised hierarchical clustering on gene expression data matrix. Pearson correlation and average were used as similarity measure and linking method, respectively.

Article Snippet: In particular, raw microarray data (Affymetrix .CEL files) were obtained for a total of 24 samples from 8 different cell types of all myelopoietic lineages, representing a reference dataset for a comprehensive analysis of genomic expression during cell differentiation.

Techniques: Expressing, Microarray

Journal: bioRxiv

Article Title: Utility of a high-resolution mouse single nucleotide polymorphism microarray assessed for rodent comparative genomics

doi: 10.1101/2020.09.29.318071

Figure Lengend Snippet:

Article Snippet: Forty publicly available MDGA raw data (CEL) files were downloaded from the Center for Genome Dynamics at the Jackson Laboratory (2012, The Jackson Laboratory; ftp.jax.org/petrs/MDA/ ).

Techniques:

Journal: bioRxiv

Article Title: Utility of a high-resolution mouse single nucleotide polymorphism microarray assessed for rodent comparative genomics

doi: 10.1101/2020.09.29.318071

Figure Lengend Snippet: SNP distance-based tree of genetic relatedness of samples from the intra-genus test set (n = 27). At 9.5 MYD a pygmy mouse subspecies M. n. orangiae has SNP-based genetic distances that reflect greater genetic similarity to another pygmy mouse subspecies M. n. minutoides than the replicate MDGA data file of the same M. n. orangiae sample. MYD = Millions of years divergence, with respect to the reference Mus musculus .

Article Snippet: Forty publicly available MDGA raw data (CEL) files were downloaded from the Center for Genome Dynamics at the Jackson Laboratory (2012, The Jackson Laboratory; ftp.jax.org/petrs/MDA/ ).

Techniques: