Journal: Journal of Biological Chemistry

Article Title: Expression Profiles of Arabidopsis thaliana in Mineral Deficiencies Reveal Novel Transporters Involved in Metal Homeostasis

doi: 10.1074/jbc.m309338200

Figure Lengend Snippet: FIG. 6. Functional characterization of AtOPT3. A, hybridization of an 600-bp AtOPT3 cDNA probe, corresponding to the 3-terminal exon, to RNA extracted from Arabidopsis roots of plants grown in control conditions (Ctl), copper (-Cu), manganese (-Mn), zinc (-Zn), and iron (-Fe) deficiency. The ethidium bromide-stained RNA gel is shown for quantification. B, growth of ctr1 expressing AtOPT3 on YPG-Ura plates supplemented with 10 M CuSO4 compared with the mutant transformed with the vector alone. C, growth of smf1 expressing AtOPT3 on manganese-limited medium, with and without 1 mM EGTA compared with the growth of the mutant transformed with the vector alone.

Article Snippet: Genome-wide Analysis Provides Insight into Metal Transport—We have used Affymetrix Arabidopsis DNA chips containing 8,300 genes (which cover about one-third of the ge- FIG. 7.

Techniques: Functional Assay, Hybridization, Control, Staining, Expressing, Mutagenesis, Transformation Assay, Plasmid Preparation

Journal: Cell Death & Disease

Article Title: The oncogene Etv5 promotes MET in somatic reprogramming and orchestrates epiblast/primitive endoderm specification during mESCs differentiation

doi: 10.1038/s41419-018-0335-1

Figure Lengend Snippet: a Comparison of Etv5 expression levels between mESC lines and somatic cell lines. The relative expression was based on the microarray data from BioGPS database. b The interactions between pluripotency relevant regulators and Etv5 . ChIP-seq and ChIP-chip data with Etv5 as target were extracted from ESCAPE database and used for drawing these interactions. c Growth curve of J1 mESCs stably infected with shCtrl and Etv5 shRNA (shEtv5-7). d RT-qPCR analysis of Etv5 and Tet2 in mESCs stably infected with shCtrl, Etv5 shRNA (shEtv5-7), and shEtv5-7 plus lentiviral Etv5 . Data are shown as mean ± SD ( n = 3). * P < 0.05, *** P < 0.001. Two-way ANOVA with Sidak’s multiple comparisons test was used for c . One-way ANOVA with Dunnett’s multiple comparisons test for d . e Western blotting of TET2 in mESCs stably infected with shCtrl, shEtv5-7, and shEtv5-7 + Etv5 . GAPDH was used as internal control. The relative quantification is also shown. f Dot blot of global 5hmC in mESCs stably infected with shCtrl, shEtv5-7, and shEtv5-7 plus lentiviral Etv5 . The blotting result of serially diluted genomic DNA (100-3.125 ng) was shown (left panel). The same membrane stained with methylene blue as DNA loading control was also presented (right panel)

Article Snippet: For transgenes integration detection, genomic DNA of mouse iPSCs was extracted using TIANamp Genomic DNA Kit (TIANGEN).

Techniques: Comparison, Expressing, Microarray, ChIP-sequencing, ChIP-chip, Stable Transfection, Infection, shRNA, Quantitative RT-PCR, Western Blot, Control, Quantitative Proteomics, Dot Blot, Membrane, Staining

Journal: Nucleic Acids Research

Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)

doi: 10.1093/nar/gkm510

Figure Lengend Snippet: Complementary-template reverse-transcription (CT-RT) of single-stranded DNA primers reverse-transcribed from FFPE-RNA. ( a ) RNA extracted from FFPE tissue is reverse-transcribed, the mRNA/DNA duplex is filtered on an YM-50 column and the DNA is single-stranded with RNase-H and column purified. The 5′-NB-Oligo-dA (24) -cT7-3′ (complementary to the T7 promoter) is annealed to the FFPE-cDNA primers. ( b ) Total RNA from universal human reference (UHR, Stratagene) is amplified using the Sense-Amp cRNA amplification kit from Genisphere to provide RNA with the same orientation as messenger RNA . ( c ) Single-stranded DNA primers are hybridized to their sense-RNA template between 70 and 42°C for 90 min. The hybridized products are reverse-transcribed by a process described as CT-RT. The restored FFPE-cDNAs are doubled stranded and transcribed in vitro using T7 polymerase. (See Supplementary Data for technical description of points 1 through 6.)

Article Snippet: Arrays used for the studies were designed and printed at the cDNA Microarray Facility, Albert Einstein College of Medicine (AECOM), Bronx, NY.

Techniques: Reverse Transcription, Purification, Amplification, In Vitro

Journal: Nucleic Acids Research

Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)

doi: 10.1093/nar/gkm510

Figure Lengend Snippet: Experimental procedure utilized for the analysis of 10-year-old matched frozen and formalin-fixed paraffin embedded breast cancer samples. ( a ) Five micrograms of RNA extracted from the 10-year-old frozen portion of the sample, is reverse-transcribed and the cDNA is double stranded (dsDNA), in four individual reactions. The dsDNA of three reactions undergoes IVT-amplification (MessageAmpII, Ambion), which gives rise to complementary RNA (cRNA) for cDNA microarray analyses. The dsDNA of one reaction is used for PCR experiments. ( b ) Five micrograms of RNA extracted from the 10-year-old FFPE portion of the sample underwent the exact same process. ( c ) Single-stranded DNA (ssDNA) obtained by RT of 5 μg of FFPE-RNA is purified and hybridized to the sense-RNA template library. The restored ssDNA is double stranded and purified. Three of the CT-RT reactions undergo IVT-amplification, while the dsDNA of one reaction is used for PCR experiments.

Article Snippet: Arrays used for the studies were designed and printed at the cDNA Microarray Facility, Albert Einstein College of Medicine (AECOM), Bronx, NY.

Techniques: Formalin-fixed Paraffin-Embedded, Reverse Transcription, Amplification, Microarray, Purification

Journal: Nucleic Acids Research

Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)

doi: 10.1093/nar/gkm510

Figure Lengend Snippet: Signal intensity and heat-map analysis of the correlation between the log 2 ratios measured by cDNA microarrays. ( a ) Signal intensity of one sample grid in the red channel (Cy5) across all microarrays. Top three panels display the grids obtained from three repeats using cRNA from 10-year-old frozen RNA (Frozen-Amp 1–3). Three mid-panels show the signal of three repeats using cRNA obtained by restoration and IVT-amplification of RNA from 10-year-old FFPE tissue (FFPE-Restored 1–3). Three bottom panels display the signal of three repeats using cRNA obtained by direct IVT-amplification of RNA from 10-year-old FFPE tissue. ( b ) Heat map displaying the log 2 of expression ratios ranging between 0.5 and 2 for 1044 genes detected in frozen tissue on a 28 032 features cDNA microarray and represented in the UHR library. From left to right are displayed the ratios obtained by IVT-amplification of RNA from 10-year-old frozen tissue (Frozen-Amp 1–3), restoration and IVT-amplification of RNA from 10-year-old FFPE tissue (FFPE-Restored 1–3) and direct IVT-amplification of RNA from 10-year-old FFPE tissue (FFPE-Amp 1–3). Each column represents an individual hybridization and each line a different feature. Red and blue represent up-regulated and down-regulated genes, respectively.

Article Snippet: Arrays used for the studies were designed and printed at the cDNA Microarray Facility, Albert Einstein College of Medicine (AECOM), Bronx, NY.

Techniques: Amplification, Expressing, Microarray, Hybridization