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    Thermo Fisher copy number variation slc6a3 mm00401145 cn
    TRAPseq analysis in a mouse model of PD and regulatory network analysis (a) Time line for TRAPseq analysis of midbrain DA neurons after injection of <t>Dat</t> bacTRAP mice with MPTP (n=4) or saline (vehicle; n=4).(b) Comparative analysis of the translatome libraries obtained from unperturbed midbrain DA neurons in saline-treated Dat bacTRAP mice (n=4) or from DA neurons under toxin-induced stress in MPTP-treated Dat bacTRAP mice (n=4). Log2 fold change values were plotted against mean gene expression values. The center line represents equal expression. Green dots represent transcripts with a ≥1.5fold increased expression in MPTP-treated samples ( P
    Copy Number Variation Slc6a3 Mm00401145 Cn, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Identification of Neurodegenerative Factors Using Translatome-Regulatory Network Analysis"

    Article Title: Identification of Neurodegenerative Factors Using Translatome-Regulatory Network Analysis

    Journal: Nature neuroscience

    doi: 10.1038/nn.4070

    TRAPseq analysis in a mouse model of PD and regulatory network analysis (a) Time line for TRAPseq analysis of midbrain DA neurons after injection of Dat bacTRAP mice with MPTP (n=4) or saline (vehicle; n=4).(b) Comparative analysis of the translatome libraries obtained from unperturbed midbrain DA neurons in saline-treated Dat bacTRAP mice (n=4) or from DA neurons under toxin-induced stress in MPTP-treated Dat bacTRAP mice (n=4). Log2 fold change values were plotted against mean gene expression values. The center line represents equal expression. Green dots represent transcripts with a ≥1.5fold increased expression in MPTP-treated samples ( P
    Figure Legend Snippet: TRAPseq analysis in a mouse model of PD and regulatory network analysis (a) Time line for TRAPseq analysis of midbrain DA neurons after injection of Dat bacTRAP mice with MPTP (n=4) or saline (vehicle; n=4).(b) Comparative analysis of the translatome libraries obtained from unperturbed midbrain DA neurons in saline-treated Dat bacTRAP mice (n=4) or from DA neurons under toxin-induced stress in MPTP-treated Dat bacTRAP mice (n=4). Log2 fold change values were plotted against mean gene expression values. The center line represents equal expression. Green dots represent transcripts with a ≥1.5fold increased expression in MPTP-treated samples ( P

    Techniques Used: Injection, Direct Antiglobulin Test, Mouse Assay, Expressing

    Analysis of MR expression patterns in midbrain DA neurons (a) MR expression levels in TRAPseq samples from either SNpc or VTA DA neurons obtained from Dat bacTRAP mice (n=6). P =0.862 ( Foxm1 ); P =0.042 ( Nr1d1 ); P =0.094 ( Olig1 ); P =0.014 ( Zdhhc13 ); P =0.0001 ( Elmsan1 ); P =0.740 ( Rax ); P =0.005 ( Tcf20 ); P =0.0004 ( Hcfc1 ); P =0.317 ( Snai1 ); P =0.214 ( Zfp341 ); P =0.210 ( Zfp612 ); P =0.002 ( Zfp473 ); P =0.754 ( Mecp2 ); P =0.003 ( Camta1 ); P =0.001 ( Dennd4a ); P =0.0001 ( Zdhhc2 ); P =0.186 ( Mef2a ); P =0.733 ( Zfp780b ); P =0.0001 ( Satb1 ). Paired t-test. FPKM, fragments per kilobase per million. (b) Coronal brain sections from WT mice stained for TH (red) and SATB1 (green). White lines indicate the border between SNpc and VTA. (c) SNpc DA neurons in WT mice stained for TH (red) and SATB1 (green) with DAPI counterstain (blue). (d) Coronal brain sections from WT mice stained for TH (red) and ZDHHC2 (green). White lines indicate the border between SNpc and VTA. (e) SNpc DA neurons in WT mice stained for TH (red), ZDHHC2 (green) and the Golgi marker GM130 (orange). White arrow heads indicate signal for ZDHHC2 that does not co-localize with that for TH. (f, g), Quantification of SATB1 and ZDHHC2 protein levels in midbrain from WT mice injected with either saline (n=4) or MPTP (n=4) according to Fig. 2a . GAPDH and β-tubulin, respectively, were used as loading controls. The molecular weight standard is shown on the right of the blot. SATB1: P =0.374; ZDHHC2: P =0.118. Unpaired t-test. Blot images are cropped. Full-length blots are presented in Supplementary Figure 9f-i . n-values indicate biological replicates. Data in (a) and (g) represent means ± SEM. Scale bars, 100 μm in (b) and (d) and 10 μm in (c) and (e). * P
    Figure Legend Snippet: Analysis of MR expression patterns in midbrain DA neurons (a) MR expression levels in TRAPseq samples from either SNpc or VTA DA neurons obtained from Dat bacTRAP mice (n=6). P =0.862 ( Foxm1 ); P =0.042 ( Nr1d1 ); P =0.094 ( Olig1 ); P =0.014 ( Zdhhc13 ); P =0.0001 ( Elmsan1 ); P =0.740 ( Rax ); P =0.005 ( Tcf20 ); P =0.0004 ( Hcfc1 ); P =0.317 ( Snai1 ); P =0.214 ( Zfp341 ); P =0.210 ( Zfp612 ); P =0.002 ( Zfp473 ); P =0.754 ( Mecp2 ); P =0.003 ( Camta1 ); P =0.001 ( Dennd4a ); P =0.0001 ( Zdhhc2 ); P =0.186 ( Mef2a ); P =0.733 ( Zfp780b ); P =0.0001 ( Satb1 ). Paired t-test. FPKM, fragments per kilobase per million. (b) Coronal brain sections from WT mice stained for TH (red) and SATB1 (green). White lines indicate the border between SNpc and VTA. (c) SNpc DA neurons in WT mice stained for TH (red) and SATB1 (green) with DAPI counterstain (blue). (d) Coronal brain sections from WT mice stained for TH (red) and ZDHHC2 (green). White lines indicate the border between SNpc and VTA. (e) SNpc DA neurons in WT mice stained for TH (red), ZDHHC2 (green) and the Golgi marker GM130 (orange). White arrow heads indicate signal for ZDHHC2 that does not co-localize with that for TH. (f, g), Quantification of SATB1 and ZDHHC2 protein levels in midbrain from WT mice injected with either saline (n=4) or MPTP (n=4) according to Fig. 2a . GAPDH and β-tubulin, respectively, were used as loading controls. The molecular weight standard is shown on the right of the blot. SATB1: P =0.374; ZDHHC2: P =0.118. Unpaired t-test. Blot images are cropped. Full-length blots are presented in Supplementary Figure 9f-i . n-values indicate biological replicates. Data in (a) and (g) represent means ± SEM. Scale bars, 100 μm in (b) and (d) and 10 μm in (c) and (e). * P

    Techniques Used: Expressing, Direct Antiglobulin Test, Mouse Assay, Staining, Marker, Injection, Molecular Weight

    Virus-mediated knockdown of SATB1 in SNpc DA neurons (a) Schematic illustration of bilateral stereotaxic AAV1 injections into the SNpc of WT mice using a Satb1 shRNA-EGFP construct (ipsilateral side) or a scrambled shRNA-EGFP construct (contralateral side; control). (b) Coronal brain section from WT mice two weeks post-injection according to panel (a) showing staining for TH (red) and EGFP autofluorescence (green). (c) Coronal brain section from WT mice two weeks post-injection according to panel (a) showing staining for TH (red) and SATB1 (orange) as well as EGFP autofluorescence (green). (d) Coronal brain section from WT mice three weeks post-injection according to panel (a) showing staining for TH (red) and EGFP autofluorescence (green). (e) GSEA of SATB1 target genes (vertical bars) on a ranked list of genes differentially expressed after Satb1 silencing in Dat bacTRAP mice according to (a) (n=3), sorted by their t-statistics. Genes that are downregulated after Satb1 silencing received high rank numbers and are displayed in the right part of the plot. The blue line in the upper part of the plot indicates the GSEA enrichment running score. Scale bars, 200 μm in (b) and (d) and 50 μm in (c). n-values indicate biological replicates .
    Figure Legend Snippet: Virus-mediated knockdown of SATB1 in SNpc DA neurons (a) Schematic illustration of bilateral stereotaxic AAV1 injections into the SNpc of WT mice using a Satb1 shRNA-EGFP construct (ipsilateral side) or a scrambled shRNA-EGFP construct (contralateral side; control). (b) Coronal brain section from WT mice two weeks post-injection according to panel (a) showing staining for TH (red) and EGFP autofluorescence (green). (c) Coronal brain section from WT mice two weeks post-injection according to panel (a) showing staining for TH (red) and SATB1 (orange) as well as EGFP autofluorescence (green). (d) Coronal brain section from WT mice three weeks post-injection according to panel (a) showing staining for TH (red) and EGFP autofluorescence (green). (e) GSEA of SATB1 target genes (vertical bars) on a ranked list of genes differentially expressed after Satb1 silencing in Dat bacTRAP mice according to (a) (n=3), sorted by their t-statistics. Genes that are downregulated after Satb1 silencing received high rank numbers and are displayed in the right part of the plot. The blue line in the upper part of the plot indicates the GSEA enrichment running score. Scale bars, 200 μm in (b) and (d) and 50 μm in (c). n-values indicate biological replicates .

    Techniques Used: Mouse Assay, shRNA, Construct, Injection, Staining, Direct Antiglobulin Test

    Generation of Dat bacTRAP mice for the translational profiling of midbrain DA neurons (a) Sagittal brain section from a Dat bacTRAP mouse stained for TH (red) and EGFP (green) at the level of the SNpc. (b) Sagittal brain section from a Dat bacTRAP mouse stained for TH (red) and EGFP (green) at the level of the VTA. (c) Mean gene expression values obtained from whole midbrain total RNA samples (n=5) plotted against mean gene expression values from midbrain DA neuron TRAP samples (n=4). Lines to each side represent 1.5fold enrichment in either sample. The center line represents equal expression. Red dots represent transcripts enriched in the DA neuron TRAP samples by ≥1.5fold ( P
    Figure Legend Snippet: Generation of Dat bacTRAP mice for the translational profiling of midbrain DA neurons (a) Sagittal brain section from a Dat bacTRAP mouse stained for TH (red) and EGFP (green) at the level of the SNpc. (b) Sagittal brain section from a Dat bacTRAP mouse stained for TH (red) and EGFP (green) at the level of the VTA. (c) Mean gene expression values obtained from whole midbrain total RNA samples (n=5) plotted against mean gene expression values from midbrain DA neuron TRAP samples (n=4). Lines to each side represent 1.5fold enrichment in either sample. The center line represents equal expression. Red dots represent transcripts enriched in the DA neuron TRAP samples by ≥1.5fold ( P

    Techniques Used: Direct Antiglobulin Test, Mouse Assay, Staining, Expressing

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    Expressing:

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    Hybridization:

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    Sequencing:

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    TaqMan Copy Number Assay:

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    Digital PCR:

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    Generated:

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    other:

    Article Title: Gene dosage as a relevant mechanism contributing to the determination of ovarian function in Turner syndrome
    Article Snippet: The target TaqMan Copy Number mixes were chosen to detect: exon 8 (Hs01858886_cn) of the GYG2 gene (MIM *300198, at Xp22.3); exon 1 (Hs01299108_cn) and exon 2 (HS00957878_cn) of the BMP15 gene (MIM *300247, at Xp11.22); exon 10 (Hs05613398_cn) of the SMARCA1 gene (MIM *300012, at Xq26.1); exon 2 (Hs02373345_cn) and exon 7 (Hs01648393_cn) of the PAPPA gene (MIM *176385, at 9q33.1); intron 2 (Hs03902365) and exon 21 (Hs03005502_cn) of the PDE8A gene (MIM *602972, at 15q25.3); and exon 9 (Hs02909158_cn) of the PRKX gene (MIM *300083, at Xp22.33).

    Article Title: Specific amplifications and copy number decreases during human neural stem cells differentiation towards astrocytes, neurons and oligodendrocytes
    Article Snippet: TaqMan Copy Number Assays for genes CDK4 (Hs00957586_cn), MDM2 (Hs00181272_cn), GINS2 (Hs05472641_cn), TP53 (Hs05506931_cn), DDB1 (Hs07226265_cn), EGFR (Hs01463609_cn), MDM4 (Hs05784087_cn), GFAP (Hs01144882_cn) were performed following manufacturers instructions.

    Article Title: FGFR2 gene amplification and clinicopathological features in gastric cancer
    Article Snippet: The primer IDs used for FGFRs were as follows: FGFR1, Hs02862256_cn; FGFR2, HS05182482_cn (intron 14) and Hs05114211_cn (intron 12); FGFR3, Hs03518314_cn; and FGFR4 , Hs01949336_cn.

    Article Title: The Microwell Control of Embryoid Body Size in order to Regulate Cardiac Differentiation of Human Embryonic Stem Cells
    Article Snippet: TaqMan Primers for GAPDH (Hs99999905_m1), NKX2-5 (Hs00231763_m1), TNNT2 (Hs00165960_m1), MYL7 (Hs00221909_ml) and PLN (Hs00160179_m1) were used.

    Article Title: NOXA genetic amplification or pharmacologic induction primes lymphoma cells to BCL2 inhibitor-induced cell death
    Article Snippet: Briefly, 20 ng of 4 μL DNA (5 ng/μL) was mixed with TaqMan Genotyping Master Mix (4371353), BCL2 (Hs01500302_cn), or PMAIP1 (Hs01670847) TaqTaqMan Copy Number Assay (20×), human TaqMan Copy Number Reference Assay RNase P (4401631) in 96-well plate.

    Polymerase Chain Reaction:

    Article Title: BRAF, GNAQ, and GNA11 mutations and copy number in pediatric low-grade glioma
    Article Snippet: 4.5 For quantitative detection of the BRAF gene, the relative dosage was determined using an ABI 7500 real-time PCR system (Applied Biosystems). .. The 15-l reaction mixture contained FAM-labeled 1x TaqMan® BRAF kit (ABI, Hs05004157_CN), VIC-labeled 1x TaqMan® Human RNase P detection mix (ABI, Cat. No. 431684906018), 1x TaqMan Universal PCR Master Mix (AmpliTaq Gold® DNA Polymerase, dNTPs with dUTP, Passive Reference, No AmpErase UNG®), and 5 ng genomic DNA template. .. RNaseP , a single-copy gene, was used as an endogenous control.

    Article Title: HPV positive neuroendocrine cervical cancer cells are dependent on Myc but not E6/E7 viral oncogenes
    Article Snippet: Myc copy number was measured by human Myc TaqMan CPopy Number Assay (Thermo Fisher # Hs01764918_cn. .. Myc copy number was measured by human Myc TaqMan CPopy Number Assay (Thermo Fisher # Hs01764918_cn.

    Article Title: Fibroblast growth factor receptor 2 expression, but not its genetic amplification, is associated with tumor growth and worse survival in esophagogastric junction adenocarcinoma
    Article Snippet: Tumor DNA was analyzed with TaqMan Copy Number Assays (Life Technologies) using Hs05182482_cn (intron 14 of FGFR2 , amplicon length 80 bp; Life Technologies) as primers. .. Tumor DNA was analyzed with TaqMan Copy Number Assays (Life Technologies) using Hs05182482_cn (intron 14 of FGFR2 , amplicon length 80 bp; Life Technologies) as primers.

    Software:

    Article Title: Massively parallel sequencing of phyllodes tumours of the breast reveals actionable mutations, and TERT promoter hotspot mutations and TERT gene amplification as likely drivers of progression
    Article Snippet: Copy number variations affecting the TERT gene were further validated using the TaqMan copy number assay (IDs: Hs06005815_cn; Applied Biosystems) on the StepOnePlus Real-Time PCR System (Applied Biosystems) as per the manufacturer’s guidelines. .. Copy number variations affecting the TERT gene were further validated using the TaqMan copy number assay (IDs: Hs06005815_cn; Applied Biosystems) on the StepOnePlus Real-Time PCR System (Applied Biosystems) as per the manufacturer’s guidelines.

    Article Title: HPV positive neuroendocrine cervical cancer cells are dependent on Myc but not E6/E7 viral oncogenes
    Article Snippet: Myc copy number was measured by human Myc TaqMan CPopy Number Assay (Thermo Fisher # Hs01764918_cn. .. Realtime PCR reactions were done in triplicate for all samples.

    Article Title: SNPs Array Karyotyping Reveals a Novel Recurrent 20p13 Amplification in Primary Myelofibrosis
    Article Snippet: In particular, the target copy number was assessed with a specific TaqMan Copy Number Assay (Hs04039030_cn; Applied Biosystems; Foster City, CA) and TaqMan Copy Number Reference Assay RNase P (Applied Biosystems). .. In particular, the target copy number was assessed with a specific TaqMan Copy Number Assay (Hs04039030_cn; Applied Biosystems; Foster City, CA) and TaqMan Copy Number Reference Assay RNase P (Applied Biosystems).

    Article Title: Insulin-Like Growth Factor 1 Receptor and Response to Anti-IGF1R Antibody Therapy in Osteosarcoma
    Article Snippet: To determine the IGF1R copy number, quantitative PCR was performed using three different Taqman copy number (CN) assays (Life Technologies, Carlsbad, CA; Assay IDs: Hs00401826_cn, Hs01239357_cn, Hs02543373_cn) targeting different locations on the chromosome 15 where the IGF1R gene spans. .. To determine the IGF1R copy number, quantitative PCR was performed using three different Taqman copy number (CN) assays (Life Technologies, Carlsbad, CA; Assay IDs: Hs00401826_cn, Hs01239357_cn, Hs02543373_cn) targeting different locations on the chromosome 15 where the IGF1R gene spans.

    Mutagenesis:

    Article Title: Somatic GPR101 Duplication Causing X-Linked Acrogigantism (XLAG)—Diagnosis and Management
    Article Snippet: After the recent description of germline Xq26.3 microduplication in young children with acrogigantism , likely due to the duplicated GPR101 gene within this region, we tested the patient's leukocyte-, saliva-, and buccal cell-derived DNA using a comparative genomic hybridization array (BlueGnome CytoChip ISCA 8 × 60k v2.0; Illumina) and copy number variation droplet digital PCR for GPR101 (Taqman assays Hs01818174_cn and Hs01730605_cn; Life Technologies) without evidence of Xq26.3 microduplications or GPR101 duplication, although his clinical phenotype was identical to the previously published patients. .. We therefore tested DNA isolated from the hyperplastic pituitary tissue and found duplicated dosage of GPR101 ( ).

    Isolation:

    Article Title: Autism gene Ube3a and seizures impair sociability by repressing VTA Cbln1
    Article Snippet: To determine transgenic Ube3a copy number, genomic DNA was isolated from mouse tail clips using the Purelink Genomic DNA Mini Kit (ThermoFisher). .. Real-time quantitative PCR was performed to measure genomic copies of Ube3a and Tfrc (transferrin receptor) using Taqman® Mm00238405_cn probe (Ube3a) and Taqman® Copy Number Reference Assay (Tfrc) with Taqman® Genotyping Master Mix (ThermoFisher).

    Article Title: Overexpression of MAPK15 in gastric cancer is associated with copy number gain and contributes to the stability of c-Jun
    Article Snippet: DNA copy number of MAPK15 in 16 gastric cancer cell lines and 48 gastric cancers were detected using commercially available, predesigned TaqMan Copy Number Assay (Assay ID: Hs00233516_cn, consisting of a pair of unlabeled primers and a FAM labeled MGB probe) and RNase P Copy Number Reference Assay (consisting of a pair of unlabeled primers and a VIC-labeled TAMRA probe) (Applied Biosystems) as previously described [ , ]. .. Tumor and non-tumorous areas were carefully microdissected under a microscope.

    Microscopy:

    Article Title: Overexpression of MAPK15 in gastric cancer is associated with copy number gain and contributes to the stability of c-Jun
    Article Snippet: DNA copy number of MAPK15 in 16 gastric cancer cell lines and 48 gastric cancers were detected using commercially available, predesigned TaqMan Copy Number Assay (Assay ID: Hs00233516_cn, consisting of a pair of unlabeled primers and a FAM labeled MGB probe) and RNase P Copy Number Reference Assay (consisting of a pair of unlabeled primers and a VIC-labeled TAMRA probe) (Applied Biosystems) as previously described [ , ]. .. The tissue sections were placed on slides and stained with H & E to evaluate the admixture of tumorous and non-tumorous tissues, before DNA was extracted from the fresh-frozen tissues.

    Mouse Assay:

    Article Title: Autism gene Ube3a and seizures impair sociability by repressing VTA Cbln1
    Article Snippet: Paragraph title: Mice ... Real-time quantitative PCR was performed to measure genomic copies of Ube3a and Tfrc (transferrin receptor) using Taqman® Mm00238405_cn probe (Ube3a) and Taqman® Copy Number Reference Assay (Tfrc) with Taqman® Genotyping Master Mix (ThermoFisher).

    Transgenic Assay:

    Article Title: Autism gene Ube3a and seizures impair sociability by repressing VTA Cbln1
    Article Snippet: To determine transgenic Ube3a copy number, genomic DNA was isolated from mouse tail clips using the Purelink Genomic DNA Mini Kit (ThermoFisher). .. Real-time quantitative PCR was performed to measure genomic copies of Ube3a and Tfrc (transferrin receptor) using Taqman® Mm00238405_cn probe (Ube3a) and Taqman® Copy Number Reference Assay (Tfrc) with Taqman® Genotyping Master Mix (ThermoFisher).

    Quantitative RT-PCR:

    Article Title: p38? Mitogen-Activated Protein Kinase Depletion and Repression of Signal Transduction to Translation Machinery by miR-124 and -128 in Neurons
    Article Snippet: Paragraph title: Quantitative reverse transcription-PCR (qRT-PCR). ... RT reactions were performed using TaqMan reverse transcription kit or miRNA reverse transcription kit (Invitrogen) followed by TaqMan qPCR (Invitrogen) on a LightCycler 480 (Roche).

    TaqMan Assay:

    Article Title: Expression of proto-oncogene KIT is up-regulated in subset of human meningiomas
    Article Snippet: SDS 7500™ Software v2.0.3 was used to analyze the data and heat map was generated using Data Assist™ Software v2.0 (ABI). .. Copy number of KIT was assessed using a commercial pre-designed TaqMan® assay (Hs02812715_cn; ABI) and RNase P as the reference gene (TaqMan® RNase P detection kit P/N: 4316831, ABI) on 7500 Real-Time PCR System (ABI). .. Tumor DNA comprised the test samples.

    Enzyme-linked Immunosorbent Assay:

    Article Title: Identification of a Shared Cytochrome p4502E1 Epitope Found in Anesthetic Drug-Induced and Viral Hepatitis
    Article Snippet: Livers were homogenized in 10% (wt/vol) RPMI-2% FCS , and cytokines were measured by ELISA (R & D Systems, Minneapolis, MN) and standardized per gram of tissue. .. Liver mRNA was analyzed (mouse inflammation panel, TaqMan qPCR array; Thermo Fisher)

    Negative Control:

    Article Title: Contamination of human DNA samples with mouse DNA can lead to false detection of XMRV-like sequences
    Article Snippet: The same DNA served as positive control in each assay, which also included a no-template negative control. .. Quality of DNA was assessed using a TaqMan qPCR for the ribosomal 18 S gene in the same reaction (Applied Biosystems).

    Labeling:

    Article Title: Overexpression of MAPK15 in gastric cancer is associated with copy number gain and contributes to the stability of c-Jun
    Article Snippet: The MLPA PCR reactions were separated on a capillary electrophoresis system ABI-Prism 3130 (Applied Biosystems, Foster City, CA), and the data was analyzed using the GeneMaker 2.0.0 (SoftGenetics, State College, PA). .. DNA copy number of MAPK15 in 16 gastric cancer cell lines and 48 gastric cancers were detected using commercially available, predesigned TaqMan Copy Number Assay (Assay ID: Hs00233516_cn, consisting of a pair of unlabeled primers and a FAM labeled MGB probe) and RNase P Copy Number Reference Assay (consisting of a pair of unlabeled primers and a VIC-labeled TAMRA probe) (Applied Biosystems) as previously described [ , ]. .. Genomic DNA was isolated using a DNA Mini Kit (Qiagen, Valencia, CA) for cell lines.

    BAC Assay:

    Article Title: Autism gene Ube3a and seizures impair sociability by repressing VTA Cbln1
    Article Snippet: BAC DNA was prepared using a Nucleobond BAC maxi-preparation kit (Clontech) and validated by sequencing analysis. .. Real-time quantitative PCR was performed to measure genomic copies of Ube3a and Tfrc (transferrin receptor) using Taqman® Mm00238405_cn probe (Ube3a) and Taqman® Copy Number Reference Assay (Tfrc) with Taqman® Genotyping Master Mix (ThermoFisher).

    Staining:

    Article Title: Overexpression of MAPK15 in gastric cancer is associated with copy number gain and contributes to the stability of c-Jun
    Article Snippet: DNA copy number of MAPK15 in 16 gastric cancer cell lines and 48 gastric cancers were detected using commercially available, predesigned TaqMan Copy Number Assay (Assay ID: Hs00233516_cn, consisting of a pair of unlabeled primers and a FAM labeled MGB probe) and RNase P Copy Number Reference Assay (consisting of a pair of unlabeled primers and a VIC-labeled TAMRA probe) (Applied Biosystems) as previously described [ , ]. .. Genomic DNA was isolated using a DNA Mini Kit (Qiagen, Valencia, CA) for cell lines.

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    Thermo Fisher copy number variation slc6a3 mm00401145 cn
    TRAPseq analysis in a mouse model of PD and regulatory network analysis (a) Time line for TRAPseq analysis of midbrain DA neurons after injection of <t>Dat</t> bacTRAP mice with MPTP (n=4) or saline (vehicle; n=4).(b) Comparative analysis of the translatome libraries obtained from unperturbed midbrain DA neurons in saline-treated Dat bacTRAP mice (n=4) or from DA neurons under toxin-induced stress in MPTP-treated Dat bacTRAP mice (n=4). Log2 fold change values were plotted against mean gene expression values. The center line represents equal expression. Green dots represent transcripts with a ≥1.5fold increased expression in MPTP-treated samples ( P
    Copy Number Variation Slc6a3 Mm00401145 Cn, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TRAPseq analysis in a mouse model of PD and regulatory network analysis (a) Time line for TRAPseq analysis of midbrain DA neurons after injection of Dat bacTRAP mice with MPTP (n=4) or saline (vehicle; n=4).(b) Comparative analysis of the translatome libraries obtained from unperturbed midbrain DA neurons in saline-treated Dat bacTRAP mice (n=4) or from DA neurons under toxin-induced stress in MPTP-treated Dat bacTRAP mice (n=4). Log2 fold change values were plotted against mean gene expression values. The center line represents equal expression. Green dots represent transcripts with a ≥1.5fold increased expression in MPTP-treated samples ( P

    Journal: Nature neuroscience

    Article Title: Identification of Neurodegenerative Factors Using Translatome-Regulatory Network Analysis

    doi: 10.1038/nn.4070

    Figure Lengend Snippet: TRAPseq analysis in a mouse model of PD and regulatory network analysis (a) Time line for TRAPseq analysis of midbrain DA neurons after injection of Dat bacTRAP mice with MPTP (n=4) or saline (vehicle; n=4).(b) Comparative analysis of the translatome libraries obtained from unperturbed midbrain DA neurons in saline-treated Dat bacTRAP mice (n=4) or from DA neurons under toxin-induced stress in MPTP-treated Dat bacTRAP mice (n=4). Log2 fold change values were plotted against mean gene expression values. The center line represents equal expression. Green dots represent transcripts with a ≥1.5fold increased expression in MPTP-treated samples ( P

    Article Snippet: Analyses were carried out with Taqman Universal PCR Master Mix (Life Technologies, #4304437) and a Taqman Slc6a3 copy number assay (FAM) (Life Technologies, Mm00401145_cn).

    Techniques: Injection, Direct Antiglobulin Test, Mouse Assay, Expressing

    Analysis of MR expression patterns in midbrain DA neurons (a) MR expression levels in TRAPseq samples from either SNpc or VTA DA neurons obtained from Dat bacTRAP mice (n=6). P =0.862 ( Foxm1 ); P =0.042 ( Nr1d1 ); P =0.094 ( Olig1 ); P =0.014 ( Zdhhc13 ); P =0.0001 ( Elmsan1 ); P =0.740 ( Rax ); P =0.005 ( Tcf20 ); P =0.0004 ( Hcfc1 ); P =0.317 ( Snai1 ); P =0.214 ( Zfp341 ); P =0.210 ( Zfp612 ); P =0.002 ( Zfp473 ); P =0.754 ( Mecp2 ); P =0.003 ( Camta1 ); P =0.001 ( Dennd4a ); P =0.0001 ( Zdhhc2 ); P =0.186 ( Mef2a ); P =0.733 ( Zfp780b ); P =0.0001 ( Satb1 ). Paired t-test. FPKM, fragments per kilobase per million. (b) Coronal brain sections from WT mice stained for TH (red) and SATB1 (green). White lines indicate the border between SNpc and VTA. (c) SNpc DA neurons in WT mice stained for TH (red) and SATB1 (green) with DAPI counterstain (blue). (d) Coronal brain sections from WT mice stained for TH (red) and ZDHHC2 (green). White lines indicate the border between SNpc and VTA. (e) SNpc DA neurons in WT mice stained for TH (red), ZDHHC2 (green) and the Golgi marker GM130 (orange). White arrow heads indicate signal for ZDHHC2 that does not co-localize with that for TH. (f, g), Quantification of SATB1 and ZDHHC2 protein levels in midbrain from WT mice injected with either saline (n=4) or MPTP (n=4) according to Fig. 2a . GAPDH and β-tubulin, respectively, were used as loading controls. The molecular weight standard is shown on the right of the blot. SATB1: P =0.374; ZDHHC2: P =0.118. Unpaired t-test. Blot images are cropped. Full-length blots are presented in Supplementary Figure 9f-i . n-values indicate biological replicates. Data in (a) and (g) represent means ± SEM. Scale bars, 100 μm in (b) and (d) and 10 μm in (c) and (e). * P

    Journal: Nature neuroscience

    Article Title: Identification of Neurodegenerative Factors Using Translatome-Regulatory Network Analysis

    doi: 10.1038/nn.4070

    Figure Lengend Snippet: Analysis of MR expression patterns in midbrain DA neurons (a) MR expression levels in TRAPseq samples from either SNpc or VTA DA neurons obtained from Dat bacTRAP mice (n=6). P =0.862 ( Foxm1 ); P =0.042 ( Nr1d1 ); P =0.094 ( Olig1 ); P =0.014 ( Zdhhc13 ); P =0.0001 ( Elmsan1 ); P =0.740 ( Rax ); P =0.005 ( Tcf20 ); P =0.0004 ( Hcfc1 ); P =0.317 ( Snai1 ); P =0.214 ( Zfp341 ); P =0.210 ( Zfp612 ); P =0.002 ( Zfp473 ); P =0.754 ( Mecp2 ); P =0.003 ( Camta1 ); P =0.001 ( Dennd4a ); P =0.0001 ( Zdhhc2 ); P =0.186 ( Mef2a ); P =0.733 ( Zfp780b ); P =0.0001 ( Satb1 ). Paired t-test. FPKM, fragments per kilobase per million. (b) Coronal brain sections from WT mice stained for TH (red) and SATB1 (green). White lines indicate the border between SNpc and VTA. (c) SNpc DA neurons in WT mice stained for TH (red) and SATB1 (green) with DAPI counterstain (blue). (d) Coronal brain sections from WT mice stained for TH (red) and ZDHHC2 (green). White lines indicate the border between SNpc and VTA. (e) SNpc DA neurons in WT mice stained for TH (red), ZDHHC2 (green) and the Golgi marker GM130 (orange). White arrow heads indicate signal for ZDHHC2 that does not co-localize with that for TH. (f, g), Quantification of SATB1 and ZDHHC2 protein levels in midbrain from WT mice injected with either saline (n=4) or MPTP (n=4) according to Fig. 2a . GAPDH and β-tubulin, respectively, were used as loading controls. The molecular weight standard is shown on the right of the blot. SATB1: P =0.374; ZDHHC2: P =0.118. Unpaired t-test. Blot images are cropped. Full-length blots are presented in Supplementary Figure 9f-i . n-values indicate biological replicates. Data in (a) and (g) represent means ± SEM. Scale bars, 100 μm in (b) and (d) and 10 μm in (c) and (e). * P

    Article Snippet: Analyses were carried out with Taqman Universal PCR Master Mix (Life Technologies, #4304437) and a Taqman Slc6a3 copy number assay (FAM) (Life Technologies, Mm00401145_cn).

    Techniques: Expressing, Direct Antiglobulin Test, Mouse Assay, Staining, Marker, Injection, Molecular Weight

    Virus-mediated knockdown of SATB1 in SNpc DA neurons (a) Schematic illustration of bilateral stereotaxic AAV1 injections into the SNpc of WT mice using a Satb1 shRNA-EGFP construct (ipsilateral side) or a scrambled shRNA-EGFP construct (contralateral side; control). (b) Coronal brain section from WT mice two weeks post-injection according to panel (a) showing staining for TH (red) and EGFP autofluorescence (green). (c) Coronal brain section from WT mice two weeks post-injection according to panel (a) showing staining for TH (red) and SATB1 (orange) as well as EGFP autofluorescence (green). (d) Coronal brain section from WT mice three weeks post-injection according to panel (a) showing staining for TH (red) and EGFP autofluorescence (green). (e) GSEA of SATB1 target genes (vertical bars) on a ranked list of genes differentially expressed after Satb1 silencing in Dat bacTRAP mice according to (a) (n=3), sorted by their t-statistics. Genes that are downregulated after Satb1 silencing received high rank numbers and are displayed in the right part of the plot. The blue line in the upper part of the plot indicates the GSEA enrichment running score. Scale bars, 200 μm in (b) and (d) and 50 μm in (c). n-values indicate biological replicates .

    Journal: Nature neuroscience

    Article Title: Identification of Neurodegenerative Factors Using Translatome-Regulatory Network Analysis

    doi: 10.1038/nn.4070

    Figure Lengend Snippet: Virus-mediated knockdown of SATB1 in SNpc DA neurons (a) Schematic illustration of bilateral stereotaxic AAV1 injections into the SNpc of WT mice using a Satb1 shRNA-EGFP construct (ipsilateral side) or a scrambled shRNA-EGFP construct (contralateral side; control). (b) Coronal brain section from WT mice two weeks post-injection according to panel (a) showing staining for TH (red) and EGFP autofluorescence (green). (c) Coronal brain section from WT mice two weeks post-injection according to panel (a) showing staining for TH (red) and SATB1 (orange) as well as EGFP autofluorescence (green). (d) Coronal brain section from WT mice three weeks post-injection according to panel (a) showing staining for TH (red) and EGFP autofluorescence (green). (e) GSEA of SATB1 target genes (vertical bars) on a ranked list of genes differentially expressed after Satb1 silencing in Dat bacTRAP mice according to (a) (n=3), sorted by their t-statistics. Genes that are downregulated after Satb1 silencing received high rank numbers and are displayed in the right part of the plot. The blue line in the upper part of the plot indicates the GSEA enrichment running score. Scale bars, 200 μm in (b) and (d) and 50 μm in (c). n-values indicate biological replicates .

    Article Snippet: Analyses were carried out with Taqman Universal PCR Master Mix (Life Technologies, #4304437) and a Taqman Slc6a3 copy number assay (FAM) (Life Technologies, Mm00401145_cn).

    Techniques: Mouse Assay, shRNA, Construct, Injection, Staining, Direct Antiglobulin Test

    Generation of Dat bacTRAP mice for the translational profiling of midbrain DA neurons (a) Sagittal brain section from a Dat bacTRAP mouse stained for TH (red) and EGFP (green) at the level of the SNpc. (b) Sagittal brain section from a Dat bacTRAP mouse stained for TH (red) and EGFP (green) at the level of the VTA. (c) Mean gene expression values obtained from whole midbrain total RNA samples (n=5) plotted against mean gene expression values from midbrain DA neuron TRAP samples (n=4). Lines to each side represent 1.5fold enrichment in either sample. The center line represents equal expression. Red dots represent transcripts enriched in the DA neuron TRAP samples by ≥1.5fold ( P

    Journal: Nature neuroscience

    Article Title: Identification of Neurodegenerative Factors Using Translatome-Regulatory Network Analysis

    doi: 10.1038/nn.4070

    Figure Lengend Snippet: Generation of Dat bacTRAP mice for the translational profiling of midbrain DA neurons (a) Sagittal brain section from a Dat bacTRAP mouse stained for TH (red) and EGFP (green) at the level of the SNpc. (b) Sagittal brain section from a Dat bacTRAP mouse stained for TH (red) and EGFP (green) at the level of the VTA. (c) Mean gene expression values obtained from whole midbrain total RNA samples (n=5) plotted against mean gene expression values from midbrain DA neuron TRAP samples (n=4). Lines to each side represent 1.5fold enrichment in either sample. The center line represents equal expression. Red dots represent transcripts enriched in the DA neuron TRAP samples by ≥1.5fold ( P

    Article Snippet: Analyses were carried out with Taqman Universal PCR Master Mix (Life Technologies, #4304437) and a Taqman Slc6a3 copy number assay (FAM) (Life Technologies, Mm00401145_cn).

    Techniques: Direct Antiglobulin Test, Mouse Assay, Staining, Expressing