|
| Status |
Public on Nov 03, 2015 |
| Title |
Control stage 15 (early neurula) |
| Sample type |
RNA |
| |
|
| Source name |
Control stage 15 (early neurula)
|
| Organism |
Xenopus laevis |
| Characteristics |
developmental stage: stage 15 (early neurula)
tissue: developing embryo
treated with: ivermectin from NF stage 10 onwards
|
| Treatment protocol |
Embryos were exposed in 0.1 X MMR from NF Stage 10 to NF Stage 45 to ivermectin (Sigma), 1 µM; 2’5’-Dideoxyadenosine (Sigma), 500 µM; Forskolin, 5 µM; Melanocyte stimulating hormone release inhibiting factor, 25 µM; SHU 9119, 500 nM. All compounds were obtained from Tocris, unless otherwise noted and prepared in Millipure (18 MΩ) water unless indicated. All drug treatments were performed using embryos from mixed batches of fertilizations, using at least 3 biological replicates. Control experiments were performed using embryos in normal media (0.1X MMR).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos (collected N=10 per eppendorf tube, 5 biological replicates) washed in RNase and DNase free water were homogenized in TRIzol reagent (Life Technologies). Homogenized samples were stored at -80°C for up to one month. Total RNA was extracted according to the manufacturer’s instructions (Life Technologies).
|
| Label |
biotin
|
| Label protocol |
Affy 3’ IVT Express Kit.
|
| |
|
| Hybridization protocol |
Microarray hybridization was performed using the Affy 3’ IVT Express Kit.
|
| Scan protocol |
Affymetrix GeneChip Fluidics, ArrayStation and Scanner as per manufacture protocol
|
| Description |
Sample1.CEL
|
| Data processing |
All microarray data were analyzed using Bioconductor packages in R. The quality of hybridized arrays was assessed using Affymetrix guidelines on the basis of scaling factor, background value, mean intensity of chip, and 3’ to 5’ ratios for spike-in control transcripts. The outlier analysis was performed using unsupervised clustering and principal component analysis. All high quality arrays were normalized using the MAS5 algorithm developed by Affymetrix. The absent/present calls for the transcripts were calculated using the MAS5 algorithm. The differentially expressed transcripts were identified on basis of fold change and Affymetrix transcripts calls. Transcripts with increased abundance were considered to be those that changed >2 fold in the experimental group compared to the control group, with present call in the experimental group. Transcripts with decreased abundance were considered to be those that changed >2 fold in the experimental group compared to the control group, with present call in control group. Differentially expressed transcripts were identified using customized script in R. The list of differentially expressed genes were annotated by Affymetrix.
|
| |
|
| Submission date |
Jul 13, 2015 |
| Last update date |
Nov 13, 2022 |
| Contact name |
Christopher Martyniuk |
| E-mail(s) |
cmartyn@ufl.edu
|
| Phone |
3523173905
|
| Organization name |
University of Florida
|
| Street address |
8891 SW 79th Avenue
|
| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32608 |
| Country |
USA |
| |
|
| Platform ID |
GPL10756 |
| Series (1) |
| GSE70834 |
Serotonergic regulation of melanocyte conversion: a bioelectric network explains stochastic all-or-none hyperpigmentation |
|
