|
| Status |
Public on Dec 31, 2017 |
| Title |
Scale E16 RCAS-beta-catenin, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Scutate scale, E16, beta-catenin misexpression
|
| Organism |
Gallus gallus |
| Characteristics |
breed: White Leghorn
tissue: scutate scale
developmental stage: embryonic day 16
treatment: beta-catenin misexpression
|
| Treatment protocol |
The gene misexpression was performed by injecting RCAS viruses to the amniotic cavity and hind limb of E3 chicken embryos, or by injecting RCAS plasmid followed by electroporation. For retinoic acid delivery, 30 g of retinoic acid was injected into the amniotic cavity at E9.
|
| Growth protocol |
Fertilized eggs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Dissected tissue was extracted in Trizol reagent.
Libraries were prepared using Illumina TruSeq RNA Sample Preparation V2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Scale_E16_b-Cat
Processed data file: E16_feather_scale_all_genes_RPKM.txt
Processed data file: E16_feather_scale_keratin_genes_RPKM.txt
|
| Data processing |
Prealignment QA/QC, adaptor sequence trimming, alignment of reads (TOPHAT 2, UCSC galGal4), and postalignment QA/QC were done in Partek Flow.
Partek Genomic Suite was used for RNA-seq read quantification, normalization and differentially expressed analysis.
Genome_build: galGal4 (Gallus_gallus-4.0)
Supplementary_files_format_and_content: E16_feather_scale_all_genes_RPKM.txt: Tab-delimited text file includes RPKM values for the complete set of genes for each sample.
Supplementary_files_format_and_content: E16_feather_scale_keratin_genes_RPKM.txt: Tab-delimited text file includes RPKM values for both differentially expressed and non-differentially expressed keratin genes for each sample.
|
| |
|
| Submission date |
Sep 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ping Wu |
| E-mail(s) |
pingwu@usc.edu
|
| Phone |
6264979629
|
| Organization name |
University of Southern California
|
| Department |
Pathology
|
| Street address |
2011 Zonal Ave HMR313A
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL19787 |
| Series (2) |
| GSE87247 |
Chicken embryonic E16 scutate scale and feather samples |
| GSE87250 |
Multiple regulatory modules are required for scale-to-feather conversion |
|
| Relations |
| BioSample |
SAMN05806328 |
| SRA |
SRX2186300 |
