|
| Status |
Public on Dec 18, 2018 |
| Title |
chicken forelimb bud_PBS_3hr_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
chicken forelimb bud PBS 3hrs
|
| Organism |
Gallus gallus |
| Characteristics |
treatment: PBS
|
| Treatment protocol |
Using tungsten needle and forceps, FGF-2 soaked beads were implanted in the posteror mesoderm of HH23 Chicken limb buds about 500microns from the distal tip. Embryos were incubated for an additional 3hrs then treated tissue was harvested and flash frozen using liquid nitrogen.
|
| Growth protocol |
Fertile chicken eggs were incubated in a humidified chamber for 4 days or until embryos reached desired developmental stage (HH23).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using QIAGEN RNeasy Plus Micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned with Hisat2 alignment algorithm to release-87 of gallus gallus genome build 5
Fold changes and statistical comparisons were obtained using EdgeR
Genome_build: Galgal5 release-87
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …
|
| |
|
| Submission date |
May 18, 2018 |
| Last update date |
Dec 18, 2018 |
| Contact name |
Kerby Clyde Oberg |
| E-mail(s) |
koberg@llu.edu
|
| Organization name |
Loma Linda University
|
| Department |
Pathology and Human Anatomy
|
| Lab |
Molecular Embryopathy
|
| Street address |
24785 Stewart Street
|
| City |
Loma Linda |
| State/province |
CA |
| ZIP/Postal code |
92350 |
| Country |
USA |
| |
|
| Platform ID |
GPL19787 |
| Series (2) |
| GSE114662 |
Genome wide analysis of chick limb bud tissue treated with FGF2 for 3hrs (RNA-Seq) |
| GSE114663 |
Genome wide analysis of chick limb bud tissue treated with FGF2 for 3 hrs |
|
| Relations |
| BioSample |
SAMN09225314 |
| SRA |
SRX4101089 |
