|
| Status |
Public on May 01, 2019 |
| Title |
E15C |
| Sample type |
SRA |
| |
|
| Source name |
claw morphogenesis epidermis
|
| Organism |
Dromaius novaehollandiae |
| Characteristics |
developmental stage: Hamburger and Hamilton stage 38
tissue: claw morphogenesis epidermis
|
| Treatment protocol |
Skin samples were dissected and placed in a minimal amount of 10 mg/mL dispase and incubated at 4 degrees celsius for 13 hours to permit clean separation of epidermis.
|
| Growth protocol |
Bird eggs were incubated with rotation in a G.Q.F 1502 Sportsmen Incubator at 37.8 degrees celsius (chicken) or 35.5 degrees celsius (emu). Alligator egg incubation is described in detail in Musser et al. 2015.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a Qiagen Rneasy kit.
polyA enriched strand-specific library was constructed using a proprietary method developed by the Yale Center for Genome Analysis
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
E15C_006_GCCAAT_L008
E15C_ggemu_scaled
|
| Data processing |
Basecalls performed using CASAVA
reads mapped to chicken, emu, or alligator genomes using Tophat2 version 2.0.6. using default parameters and setting the -GTF option
read counts generated using HTSEQ version 0.5.3p9 implemented in python version 2.7.2. We set the option requiring reads to map to the correct strand, and resolved issues with multiple mappings using the option "intersection-nonempty".
TPM (transcript per million) relative expression values were calculated for all genes using the following method: Wagner GP, Kin K, Lynch VJ. 2012. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theor Biosci. 131:281-285.
We applied a scaling factor to all emu TPM values (.55x) and alligagtor TPM values (.62) to account for differences in the number of annotated genes. This value was calculated using the method outlined here: Musser, J. M. & Wagner, G. P. Character trees from transcriptome data: Origin and individuation of morphological characters and the so-called ‘species signal’. J Exp Zool (Mol Dev Evol) 324, 588–604 (2015).
Genome_build: Chicken reads were mapped to ensembl WASHUC2 release version 68. Emu reads were mapped to a preliminary version of the Emu genome generated by the Alan Baker Lab at the University of Toronto. Alligator reads were mapped to american alligator genome allmis1.
Genome_build: Chicken: WASHUC2 (https://may2012.archive.ensembl.org/Gallus_gallus/Info/Index)
Genome_build: Alligator: Allmis1 (https://hgdownload-test.gi.ucsc.edu/goldenPath/allMis1/bigZips/)
Genome_build: Emu: preliminary version from Allan Baker's Lab is not available publicly
Supplementary_files_format_and_content: the final scaled TPM values for all chicken, emu, and alligator one-to-one orthologs that were used for analyses. The matrix uses chicken gene identifiers from the WASHUC2 version of the chicken genome (the data from Emu and Alligator are only for the 1-1 orthologs to chicken).
|
| |
|
| Submission date |
Sep 26, 2018 |
| Last update date |
May 01, 2019 |
| Contact name |
Jacob Musser |
| E-mail(s) |
jmmusser@gmail.com
|
| Organization name |
European Molecular Biology Laboratory
|
| Street address |
Meyerhofstrasse 1
|
| City |
Heidelberg |
| ZIP/Postal code |
69117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22596 |
| Series (1) |
| GSE120493 |
Subdivision of ancestral scale genetic program underlies origin of feathers and avian scutate scales |
|
| Relations |
| BioSample |
SAMN10131512 |
| SRA |
SRX4740555 |
