Journal: Genome Biology

Article Title: Exon expression profiling reveals stimulus-mediated exon use in neural cells

doi: 10.1186/gb-2007-8-8-r159

Figure Lengend Snippet: Calcium-mediated changes in transcript abundance are enriched for functional gene categories. (a) Hierarchical clustering of the potassium chloride (KCl) transcript dataset identifies six major patterns of gene expression over the 24-hour time course. The number of transcripts contained in each cluster is designated in parentheses. Shown in each plot is the averaged expression behavior of all transcripts in the indicated cluster, with error bars indicating the deviation from the mean for the entire cluster. Expression behavior of each transcript was obtained by subtracting the mean of all points at all times from each expression value in the original time series, and dividing by the standard deviation. KCl-treated time points are indicated in blue. Thapsigargin (TPG) treatment is indicated in red. (b) Gene Ontology (GO) analyses of the transcripts in each cluster reveals functional enrichment in clusters T1 to T4. (c) Polymerase chain reaction performed on cDNA from treated and untreated IMR-32 cells validates changes in transcript abundance predicted by the microarray data. PREX1 , a gene whose abundance was not predicted to change, served as a normalization control. (d) Transcripts regulated by KCl stimulation at 24 hours are similarly affected by TPG treatment. Numbers indicate upregulated and downregulated transcripts. Among those transcripts affected by both KCl and TPG, 116 were upregulated and 573 were downregulated. ARRDC3 , arrestin domain containing 3; BNIP3 , BCL2 adenovirus E1B 19 kDa interacting protein 3; ETV5 , ets variant gene 5; GLI3 , GLI-Kruppel family member 3; KCNK7 , potassium channel, subfamily K, member 7; PREX1 , phosphatidylinositol 3,4,5-trisphosphate-dependent RAC exchanger 1; OVGP1 , oviductal glycoprotein 1; STC1 , stanniocalcin 1; ZNF143 , zinc finger protein 143.

Article Snippet: Human neuroblastoma IMR-32 cells (ATCC, Manassas, VA, USA) were cultured at 37°C in a humidified atmosphere with 5% carbon dioxide in Eagle's minimum essential media (EMEM; ATCC), modified to contain the following: Earle's balanced salt solution, nonessential amino acids, 2 mmol/l L-glutamine, 1 mmol/l sodium pyruvate, and 1.5 g/l sodium bicarbonate, with 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA) and penicillin/streptomycin.

Techniques: Functional Assay, Gene Expression, Expressing, Standard Deviation, Polymerase Chain Reaction, Microarray, Control, Variant Assay

Journal: Biosensors & bioelectronics

Article Title: Microarray method to monitor 40 intestinal bacterial species in the study of azo dye reduction

doi: 10.1016/j.bios.2004.04.011

Figure Lengend Snippet: Bacteria and the probe numbers in the microarray

Article Snippet: Anaerobic bacteria were cultured at 35 °C in either prereduced anaerobically sterilized (PRAS) Brain Heart Infusion (BIH) broth supplemented with vitamin K and hemin (Remel, Lenexa, KS, USA), inoculated under an oxygen-free cannula using 85% nitrogen, 10% hydrogen and 5% carbon dioxide, or on PRAS brucella blood agar plates supplemented with vitamin K and hemin (Remel). table ft1 table-wrap mode="anchored" t5 caption a7 Number Bacterial species and strain Probe number 1 B. thetaiotaomicron ATCC 29148 1, 2, 3 2 B. vulgatus ATCC 8482 4, 5, 6 3 B. fragilis ATCC 23745 7, 8, 9 4 B. distasonis ATCC 8503 10, 11, 12 5 C. clostridioforme ATCC 29084 13, 14, 15 6 C. leptum ATCC 29065 16, 17, 18 7 F. prausnitzii ATCC 27768 19, 20, 21 8 P. productus ATCC 27340 22, 23, 24 9 R. obeum ATCC 29174 25, 26, 27 10 R. bromii ATCC 27255 28, 29, 30 11 R. callidus ATCC 27760 31, 32, 33 12 R. albus ATCC 27210 34, 35, 36 13 B. longum ATCC 15707 37, 38, 39 14 B. adolescentis ATCC 15703 40, 41, 42 15 B. infantis ATCC 15697 43, 44, 45 16 E. biforme ATCC 27806 46, 47, 48 17 E. aerofaciens ATCC 25986 49, 50, 51 18 L. acidophilus ATCC 4356 52, 53, 54 19 E. coli ATCC 25922 55, 56, 57 20 E. faecium ATCC 19434 58, 59, 60 21 B. uniformis ATCC 8492 61, 62, 63 22 B. ovatus ATCC 8483 64, 65, 66 23 B. caccae ATCC 43185 67, 68, 69 24 C. perfringens ATCC 13124 70, 71, 72 25 C. butyricum ATCC 19398 73, 74, 75 26 C. ramosum ATCC 25582 76, 77, 78 27 C. difficile ATCC 9689 79, 80, 81 28 C. indolis ATCC 25771 82, 83, 84 29 F. russii ATCC 25533 85, 86, 87 30 F. nucleatum ATCC 25586 88, 89, 90 31 B. catenulatum ATCC 27539 91, 92, 93 32 B. angulatum ATCC 27535 94, 95, 96 33 E. rectale ATCC 33656 97, 98, 99 34 E. eligens ATCC 27750 100, 101, 102 35 E. limosum ATCC 8486 103, 104, 105 36 E. lentum ATCC 25553 106, 107, 108 37 L. fermentum ATCC 9338 109, 110, 111 38 E. faecalis ATCC 27274 112, 113, 114 39 P. magnus ATCC 14955 115, 116, 117 40 R. gnavus ATCC 291492 118, 119, 120 Open in a separate window Bacteria and the probe numbers in the microarray 2.2.

Techniques: Bacteria

Journal: Biosensors & bioelectronics

Article Title: Microarray method to monitor 40 intestinal bacterial species in the study of azo dye reduction

doi: 10.1016/j.bios.2004.04.011

Figure Lengend Snippet: Microarray test results read from

Article Snippet: Anaerobic bacteria were cultured at 35 °C in either prereduced anaerobically sterilized (PRAS) Brain Heart Infusion (BIH) broth supplemented with vitamin K and hemin (Remel, Lenexa, KS, USA), inoculated under an oxygen-free cannula using 85% nitrogen, 10% hydrogen and 5% carbon dioxide, or on PRAS brucella blood agar plates supplemented with vitamin K and hemin (Remel). table ft1 table-wrap mode="anchored" t5 caption a7 Number Bacterial species and strain Probe number 1 B. thetaiotaomicron ATCC 29148 1, 2, 3 2 B. vulgatus ATCC 8482 4, 5, 6 3 B. fragilis ATCC 23745 7, 8, 9 4 B. distasonis ATCC 8503 10, 11, 12 5 C. clostridioforme ATCC 29084 13, 14, 15 6 C. leptum ATCC 29065 16, 17, 18 7 F. prausnitzii ATCC 27768 19, 20, 21 8 P. productus ATCC 27340 22, 23, 24 9 R. obeum ATCC 29174 25, 26, 27 10 R. bromii ATCC 27255 28, 29, 30 11 R. callidus ATCC 27760 31, 32, 33 12 R. albus ATCC 27210 34, 35, 36 13 B. longum ATCC 15707 37, 38, 39 14 B. adolescentis ATCC 15703 40, 41, 42 15 B. infantis ATCC 15697 43, 44, 45 16 E. biforme ATCC 27806 46, 47, 48 17 E. aerofaciens ATCC 25986 49, 50, 51 18 L. acidophilus ATCC 4356 52, 53, 54 19 E. coli ATCC 25922 55, 56, 57 20 E. faecium ATCC 19434 58, 59, 60 21 B. uniformis ATCC 8492 61, 62, 63 22 B. ovatus ATCC 8483 64, 65, 66 23 B. caccae ATCC 43185 67, 68, 69 24 C. perfringens ATCC 13124 70, 71, 72 25 C. butyricum ATCC 19398 73, 74, 75 26 C. ramosum ATCC 25582 76, 77, 78 27 C. difficile ATCC 9689 79, 80, 81 28 C. indolis ATCC 25771 82, 83, 84 29 F. russii ATCC 25533 85, 86, 87 30 F. nucleatum ATCC 25586 88, 89, 90 31 B. catenulatum ATCC 27539 91, 92, 93 32 B. angulatum ATCC 27535 94, 95, 96 33 E. rectale ATCC 33656 97, 98, 99 34 E. eligens ATCC 27750 100, 101, 102 35 E. limosum ATCC 8486 103, 104, 105 36 E. lentum ATCC 25553 106, 107, 108 37 L. fermentum ATCC 9338 109, 110, 111 38 E. faecalis ATCC 27274 112, 113, 114 39 P. magnus ATCC 14955 115, 116, 117 40 R. gnavus ATCC 291492 118, 119, 120 Open in a separate window Bacteria and the probe numbers in the microarray 2.2.

Techniques: Microarray

Journal: Frontiers in Oncology

Article Title: Chaperonin containing TCP-1 (CCT/TRiC) is a novel therapeutic and diagnostic target for neuroblastoma

doi: 10.3389/fonc.2022.975088

Figure Lengend Snippet: CCT2 is detected in pediatric tumor tissues. (A) Representative IHC images of CCT2 staining using the pediatric malignant tumor tissue array with normal tissue as control (PC701, US Biomax) (n=70). The CCT2 staining score is listed below each image. (B) Representative images from CCT2 staining using the neuroblastoma and peripheral nerve tissue microarray (NB642c, US Biomax) (n=32). CCT2 stain score is listed below each image as well as CD56 and CgA scores provided with TMA. All images were taken at 40x magnification.

Article Snippet: Slides with formalin-fixed paraffin-embedded (FFPE) tissues were received from US Biomax: PC701 and NB642c.

Techniques: Staining, Microarray

Journal: Nature Communications

Article Title: INPP4B promotes PI3Kα-dependent late endosome formation and Wnt/β-catenin signaling in breast cancer

doi: 10.1038/s41467-021-23241-6

Figure Lengend Snippet: a , b Primary human breast cancer tissues and normal adjacent breast tissues from tissue microarrays (US Biomax, n = 224 cases) ( a ) or the Melbourne Collaborative Cohort Study (MCCS, n = 107 cases) ( b ) were immunostained using an INPP4B-specific monoclonal antibody. INPP4B protein expression was scored as 0 (no expression), 1 (low), 2 (moderate), and 3 (high), and correlated with breast cancer subtype. c , d Relative INPP4B mRNA expression was quantified from normal adjacent breast and primary breast cancer tissue samples using Tissue Scan Breast Cancer cDNA Arrays I-IV (OriGene) by quantitative RT-PCR using INPP4B primers ( n = 130 cases). INPP4B mRNA expression was normalized to β-ACTIN expression levels and quantified relative to the mean of the normal adjacent breast samples. c Data represent median INPP4B mRNA expression ±25th and 75th percentiles. d Altered INPP4B mRNA expression was correlated with breast cancer subtype. e , f INPP4B mRNA expression was stratified by PIK3CA , PTEN , or AKT1 mutation status ( e ), or PIK3CA mutation status and ER-positivity ( f ) in breast tumors from the METABRIC cohort ( n = 1904 cases). The center line indicates the median, the lower bound of the box indicates the 25th percentile, the upper bound of the box represent the 75th percentile, the lower whisker extends from the 25th percentile to the minimum value, and the upper whisker extends from the 75th percentile to the maximum value. p values determined by Fisher’s exact test are indicated in a , b , d , by Kruskal–Wallis test with Dunn’s post hoc test in c , f , and by two-tailed unpaired Mann–Whitney test in e .

Article Snippet: Primary human breast cancer tissue microarrays (224 breast cancers and 32 tumor-adjacent normal breast tissues) were purchased from US Biomax (BR1921a and BR2082a).

Techniques: Expressing, Quantitative RT-PCR, Mutagenesis, Whisker Assay, Two Tailed Test, MANN-WHITNEY

Journal: Genes

Article Title: Network Approaches for Charting the Transcriptomic and Epigenetic Landscape of the Developmental Origins of Health and Disease

doi: 10.3390/genes13050764

Figure Lengend Snippet: Published transcriptomic datasets within the context of early human development.

Article Snippet: Applied Biosystems Human Genome Survey Microarray (32,878 60-mer oligonucleotide) , Oocytes , Germinal vesicle, in vivo-MII and IVM-MII oocytes expressed 12,219, 9735 and 8510 genes, respectively , Characterisation of the patterns of gene expression in germinal vesicle stage and meiosis II oocytes matured in vitro or in vivo , [ ] .

Techniques: In Vivo, Expressing, Marker, Sequencing, In Vitro, Microarray, Activation Assay