idat files containing raw data from assessment of microarrays  (Illumina Inc)

Journal: BMC Genomics

Article Title: Genome-wide expression quantitative trait loci (eQTL) analysis in maize

doi: 10.1186/1471-2164-12-336

Figure Lengend Snippet: Map position of eQTL . Genetic position of the significant eQTL associations found in biological replicate 1. Genetic position of SNP marker (cM by chromosome) most significantly associated with the differential transcript abundance, x-axis. Genetic position of gene being measured by unique microarray probe, y-axis. The most significant associations (blue, KS p-value ≤ 1E -15 ) generally function in cis (diagonal line) where the eQTL and the transcript being measured map to the same genetic position. The weaker associations (pink, KS p-value ≥ 10 -15 ) generally function in trans (periphery) where the eQTL maps to a position other than the transcript being measured.

Article Snippet: The Agilent microarray expression data (raw and processed) are available from GEO (Series Accession GSE29964).

Techniques: Marker, Microarray

Journal: BMC Genomics

Article Title: Genome-wide expression quantitative trait loci (eQTL) analysis in maize

doi: 10.1186/1471-2164-12-336

Figure Lengend Snippet: Quantity and mode of action of eQTL . eQTL were categorized as cis- or trans-acting based on map positions of the eQTL as compared to the genomic origin of the gene being measured by the microarray. A total of 10,941 eQTL were identified that were analyzable for mode of action based on strict transcript genomic origin criteria. Ninety per cent of all eQTL (9,795 of 10,941) functioned through a cis regulatory mechanism. Normalizing the number of eQTL identified as cis- or trans-shows that the stronger eQTL tend to function through cis-regulation (red, n = 9,795) while weaker eQTL tend to function through trans-regulation (blue, n = 1,146).

Article Snippet: The Agilent microarray expression data (raw and processed) are available from GEO (Series Accession GSE29964).

Techniques: Microarray

Journal: BMC Genomics

Article Title: Genome-wide expression quantitative trait loci (eQTL) analysis in maize

doi: 10.1186/1471-2164-12-336

Figure Lengend Snippet: False positive cis-eQTL . Relative expression levels determined by the microarray suggests that cis-acting factors regulate the expression of two example genes. In both cases (A,B) the B73 transcript abundance is far greater than that of Mo17 according to the microarray. Amplification of genomic and cDNA sequence from B73 and Mo17 reveals that actual expression in situ may be more similar than the microarray would suggest. Sequence analysis of the probe-hybridization loci reveal that the microarray probes (red highlight) would fail to hybridize efficiently to the Mo17 alleles, thus inappropriately suggesting extreme differential expression and strong cis-eQTL. Blue boxes show polymorphisms between the Mo17-derived sequences as compared to the reference probe and B73-derived sequences.

Article Snippet: The Agilent microarray expression data (raw and processed) are available from GEO (Series Accession GSE29964).

Techniques: Expressing, Microarray, Amplification, Sequencing, In Situ, Hybridization, Derivative Assay

Journal: BMC Genomics

Article Title: Genome-wide expression quantitative trait loci (eQTL) analysis in maize

doi: 10.1186/1471-2164-12-336

Figure Lengend Snippet: Sequence gap in the physical map masks probe homology sites . A Schematic of selected maize chromosomes. A "master regulating" trans-eQTL residing on chromosome 2, BAC AC207404 (blue diamond) regulates expression of two iron superoxide dismutase genes on the long arms of chromosomes 1 (BAC AC221053) and 6 (BAC AC187242), as measured by unique microarray probes (red and cyan, respectively); centromeres = black circles . B Re-sequencing analysis of the eQTL interval on chromosome 2 revealed a 2 kb gap (gray dotted line) in the known sequence (gray bars). Probe homology sites for both regulated genes were discovered within the gap negating a trans-acting master regulator effect, therefore suggesting a strong cis-acting eQTL in the vicinity of the newly identified third iron superoxide dismutase gene.

Article Snippet: The Agilent microarray expression data (raw and processed) are available from GEO (Series Accession GSE29964).

Techniques: Sequencing, Expressing, Microarray

Journal: BMC Genomics

Article Title: Genome-wide expression quantitative trait loci (eQTL) analysis in maize

doi: 10.1186/1471-2164-12-336

Figure Lengend Snippet: Fine mapping of eQTL regulating ABA 8'-hydroxylase . A Microarray expression data revealed greater expression of the target gene ABA 8'-hydroxylase. The target gene is present in both parental backgrounds but is much more strongly expressed under control of a B73 derived allele of the trans-regulator glutamine amidotransferase. Multiple splice variants are amplified from the pseudogene cDNA. Sequence analysis of variants shows that only the smallest band is able to hybridize to the microarray probe, asterisk . Among parental controls, the B73 inbred average expression shows a 9-fold greater expression of the pseudogene as compared the Mo17 inbred. An F1 hybrid shows mid-level expression regulation of the relevant band, asterisk , as well as several others. B Example phenotypes/genotypes found within the IBM2 Syn10 population and controls. Phenotypes are considered "high" or "low" depending on the relative ABA 8'hydroxylase target gene expression levels. B73 alleles of the eQTL allow for high expression of the target as compared to Mo17 alleles; B73 derived allele = green, Mo17 derived allele = blue. Fine mapping of the IBM2 Syn10 population using molecular markers (M1-M6) identified a very small region at the 3' end of the gene as being the responsible element that determines the expression of the target. C BACs within eQTL interval with public markers (IDP markers; red) and designed mapping markers M1-M6 (teal) spanning the region (not drawn to scale). IDP3798 and two mapping markers are located within the glutamine amidotransferase gene.

Article Snippet: The Agilent microarray expression data (raw and processed) are available from GEO (Series Accession GSE29964).

Techniques: Microarray, Expressing, Derivative Assay, Amplification, Sequencing

Journal: BMC Genomics

Article Title: Genome-wide expression quantitative trait loci (eQTL) analysis in maize

doi: 10.1186/1471-2164-12-336

Figure Lengend Snippet: Unexpected expression regulation of a pseudogene results from sequence variation in the carboxy terminal of glutamine amidotransferase . A The B73 and Mo17derived sequences for the trans-regulator glutamine amidotransferase code for nearly identical proteins. Blue boxes highlight residues different from the B73 reference sequence. Fine mapping of the eQTL to a 186 bp interval determined that the carboxy-terminus accounts for the trans-regulation, black bar . Class I glutamine amidotransferase proteins require the conserved C-H-E triad (red boxes) for their expected enzymatic functions suggesting that, despite the sequence differences between the genotypes, the proteins likely remain functional in their expected pathway in situ. B Genomic structure on chromosome 1(BAC AC177817) that encodes for the pseudogene is derived from chimerization of 1.5 exons of the functional ABA 8'-hydroxylase genic region (blue bar, blue exons) of chromosome 4 (BAC AC182187), a 5' element enabling transcription originating from chromosome 10 (green bar; BAC AC194847), and genomically non-unique sequence (yellow dashed bar, yellow exons). The microarray probe (red bar) used to measure the pseudogene is unique within the transcriptome.

Article Snippet: The Agilent microarray expression data (raw and processed) are available from GEO (Series Accession GSE29964).

Techniques: Expressing, Sequencing, Functional Assay, In Situ, Derivative Assay, Microarray

Journal: Frontiers in Immunology

Article Title: Deciphering the molecular landscape of rheumatoid arthritis offers new insights into the stratified treatment for the condition

doi: 10.3389/fimmu.2024.1391848

Figure Lengend Snippet: The workflow of data processing procedures in the study. Four microarray datasets containing 1,138 RA patients and three RNA-seq datasets including 268 RA patients were selected as training sets and test sets respectively from the public database. DEGs were filtered after the normalization, and unsupervised clustering was performed with enrichment analysis followed. Then, the XGBoost algorithm was contrived to predict the responses of stratified subtypes to commonly used five treatments. Finally, in search for more novel therapeutic targets of RA patients, drug prediction was carried out by utilizing SMR and the Open Targets platform. DEGs, differentially expressed genes; SMR, Summary data-based Mendelian randomization analysis.

Article Snippet: The normalized matrix files for raw microarray data from Illumina were directly downloaded.

Techniques: Microarray, RNA Sequencing, Biomarker Discovery

Journal: Cell reports

Article Title: Circulating tumor cells reveal early predictors of disease progression in patients with stage III NSCLC undergoing chemoradiation and immunotherapy.

doi: 10.1016/j.celrep.2024.113687

Figure Lengend Snippet: Figure 1. Overview of CTC isolation and characterization summary (A) Schematic of CTC isolation using microfluidic graphene oxide (GO) chips. Each sample is processed on two devices, one for enumeration via immunoflu- orescent staining and the second for mRNA microarray analysis. The CTC characteristics are then used generate profiles that are predictive of progression-free survival. (B) The timeline of patient sample draws shown; the black time points indicate no treatment, the blue time points are during chemoradiation therapy, and green time points are during durvalumab for most patients.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CD45 BioRad Cat# MCA87, RRID: AB_871979 Alexa Fluor 488, goat anti-mouse IgG2a ThermoFisher Cat# A21131, RRID: AB_2535771 Pan-CK BioRad Cat# MCA1907, RRID: AB_2281069 Alexa Fluor 546 goat anti-mouse IgG1 ThermoFisher Cat# A21123, RRID:AB_2535765 PD-L1 BioLegend Cat# 329702, RRID: AB_940362 Alexa Fluor 647 goat anti-mouse IgG2b ThermoFisher Cat# A21242, RRID: AB_2535811 Human EpCAM/TROP-1 Biotinylated Antibody R&D Systems Cat# BAF960, RRID: AB_356818 CD133/2-Biotin, human, Clone 293C3 Miltentyi Cat # 130-113-185, RRID: AB_2726011 Anti-EGFR RayBiotech Cat# MD02-0006, RRID: AB_949700 Biological samples Human blood samples stage III NSCLC patients This paper N/A Healthy human blood samples This paper N/A Chemicals, peptides, and recombinant proteins Graphene oxide N, N-dimethylformamide (DMF) Tetrabutylammonium (TBA) hydroxide phospholipid-polyethylene–glycol-amine (PL-PEG-NH2) N-(gamma-maleimidobutyryloxy) succinimide (GMBS) Critical commercial assays Clarium S PICO Miroarrays ThermoFisher Cat# 902928 Arcturus PicoPure RNA Isolation Kit ThermoFisher Cat# KIT0204 Deposited data Microarray Raw Data This study GEO database: #24401360 Experimental models: Cell lines NCI-H1650 ATCC CRL-5883 NCI-H3255

Techniques: Isolation, Staining, Microarray

Journal: Cell reports

Article Title: Circulating tumor cells reveal early predictors of disease progression in patients with stage III NSCLC undergoing chemoradiation and immunotherapy.

doi: 10.1016/j.celrep.2024.113687

Figure Lengend Snippet: Figure 4. mRNA microarray data demonstrate altered gene expression profiles of CTCs during chemoradiation treatment (A) Unbiased clustering heatmap of top 50 differentially expressed genes by log fold change. Sample time points and patient outcome are labeled in the top rows. Patient IDs are also labeled on the bottom of the heatmap. In the right-hand annotation columns, each gene is recorded as being found in the literature to cause the given effect, including proliferation, invasion, and metastasis. See also Table S6. (B) Select genes with normalized expression for pre-TX and week 4 time points alongside healthy controls. (C) Fold change for 7 genes between pre-TX and week 4 time points that were differentially expressed in patients with sustained stable disease. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CD45 BioRad Cat# MCA87, RRID: AB_871979 Alexa Fluor 488, goat anti-mouse IgG2a ThermoFisher Cat# A21131, RRID: AB_2535771 Pan-CK BioRad Cat# MCA1907, RRID: AB_2281069 Alexa Fluor 546 goat anti-mouse IgG1 ThermoFisher Cat# A21123, RRID:AB_2535765 PD-L1 BioLegend Cat# 329702, RRID: AB_940362 Alexa Fluor 647 goat anti-mouse IgG2b ThermoFisher Cat# A21242, RRID: AB_2535811 Human EpCAM/TROP-1 Biotinylated Antibody R&D Systems Cat# BAF960, RRID: AB_356818 CD133/2-Biotin, human, Clone 293C3 Miltentyi Cat # 130-113-185, RRID: AB_2726011 Anti-EGFR RayBiotech Cat# MD02-0006, RRID: AB_949700 Biological samples Human blood samples stage III NSCLC patients This paper N/A Healthy human blood samples This paper N/A Chemicals, peptides, and recombinant proteins Graphene oxide N, N-dimethylformamide (DMF) Tetrabutylammonium (TBA) hydroxide phospholipid-polyethylene–glycol-amine (PL-PEG-NH2) N-(gamma-maleimidobutyryloxy) succinimide (GMBS) Critical commercial assays Clarium S PICO Miroarrays ThermoFisher Cat# 902928 Arcturus PicoPure RNA Isolation Kit ThermoFisher Cat# KIT0204 Deposited data Microarray Raw Data This study GEO database: #24401360 Experimental models: Cell lines NCI-H1650 ATCC CRL-5883 NCI-H3255

Techniques: Microarray, Gene Expression, Labeling, Expressing