SNX6 | bioCADDIE Data Discovery Index
Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Displaying 3 of 3 results for "SNX6"
i
  1. SNX6_PONAB UniProt:Swiss-Prot

    ID: Q5R613

    Description: Sorting nexin-6 Removed; alternate Sorting nexin-

  2. CRYSTAL STRUCTURE OF THE BRMS1 N-TERMINAL REGION PDB

    ID: PDB:2XUS

    Description: BREAST CANCER METASTASIS-SUPPRESSOR 1

    primaryPublication.title: The Structure of Brms1 Nuclear Export Signal and Snx6 Interacting Region Reveals a Hexamer Formed by Antiparallel Coiled Coils.
  3. Gene expression profiling of chickpea responses to cold stress BioProject

    ID: PRJNA105515

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: roxide dismutase precursor protein (DY475397) and sorting nexin protein (DY475523) were the only known transcripts to be consistently repressed. Keywords: Chickpea, Cold stress, Tolerant, Susceptible, cDNA microarray Overall design: Total RNA was extracted from separately pooled leaf and flowers/buds/early pods tissues for each genotype {Sonali (Tolerant1), Amethyst (Susceptible1), ILC 01276 (Tolerant2) and DOOEN (Susceptible2)} at each time-point (including control samples) using the RNeasy® Plant Mini Kit (Qiagen, Valencia, CA). The quantity and quality of the total RNA samples were assessed by OD260/OD280 ratios and gel electrophoresis respectively. Fluorescent-labeled targets were prepared and hybridized to array slides as described [Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666]. All hybridizations were performed with six technical replicates and three biological replicates, incorporating dye-swapping (i.e. reciprocal labelling of Cy3 and Cy5) to eliminate any dye bias. Overall, 288 images were analyzed from 48 genotype x tissue type x treatment/control x biological replication condition. Slides were scanned at 532 nm (Cy3 green laser) and 660 nm (Cy5 red laser) at 10 µm resolution using an Affymetrix® 428™ array scanner (Santa Clara, CA), and captured with the Affymetrix® Jaguar™ software (v. 2.0, Santa Clara, CA). Image analysis was performed using Imagene™ 5 (BioDiscovery, Marina Del Rey, CA) software. Quantified spot data was then compiled and transformed using GeneSight™ 3 (BioDiscovery, Marina Del Rey, CA). Data transformations consisted of a local background correction (mean intensity of background was subtracted from mean signal intensity for each spot), omitting flagged spots, LOWESS normalisation of the entire population, creating a Cy5/Cy3 mean signal ratio, taking a shifted log (base 2), and combination of duplicated spot data. To identify differentially expressed (DE) genes, expression ratio results were filtered to eliminate genes whose 95% confidence interval for mean fold change (FC) did not extend to 2-fold up or down, followed by Students t test with False Discovery Rate (FDR) multiple testing correction to retain only genes in which expression changes versus untreated control were significant at P < 0.05....

Displaying 3 of 3 results for "SNX6"