|
| Status |
Public on Mar 04, 2021 |
| Title |
MO 5: NSD3 Morpholino Replicate 5 |
| Sample type |
SRA |
| |
|
| Source name |
cranial neural folds
|
| Organism |
Gallus gallus |
| Characteristics |
treatment: 0.5mM NSD3 MO
developmental stage: 5-7 somite chick embryos
number of animals: Pool of 12 embryos
|
| Treatment protocol |
Hamburger and Hamilton (HH) stage 4 to 5 embryos were bilaterally electroporated with 0.5 mM mmMO or NSD3 MO and 300 ng/µL pCS2+myc (Turner and Weintraub, 1994) carrier DNA.
|
| Growth protocol |
Fertilized eggs were obtained from Sunnyside Eggs (Beaver Dam, WI) and Hoover’s Hatchery (Rudd, IA). Eggs were incubated in humidified incubators (G.Q.F. Manufacturing, Savannah, GA) at 39°C until the desired developmental stage.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cranial neural fold explants were placed in Ringer’s saline on ice for a maximum of 1 hour. Neural fold explants were homogenized in TRIzol Reagent (ThermoFisher Scientific, Waltham, MA) and stored at -80°C until bilateral cranial neural folds from 60 embryos of each condition were collected. These homogenized samples were then pooled in groups of 12, creating five biological replicates for each condition. Total RNA was isolated by TRIzol extraction, then cleaned by following the RNA Cleanup protocol with RNeasy spin columns (QIAGEN, Velencia, CA).
Poly(A)+ RNA was selected from total RNA using the Illumina TruSeq stranded mRNA kit (San Diego, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were trimmed with Trimmomatic (version 0.32) and mapped to the Gallus_gallus GRCg6a genome (Ensembl) using STAR (version 2.5.3a).
Gene abundance estimates were determined with Ensembl version 100 annotations for Galgal6 using Rsubread (version 1.28.1).
Differential gene expression was determined with DESeq2 ( version 1.28.1)
Genome_build: GRCg6a
Supplementary_files_format_and_content: xlsx: lists of differentially expressed genes and FPKM values; bigWig: genome wide transcript coverage data.
|
| |
|
| Submission date |
Nov 16, 2020 |
| Last update date |
Mar 04, 2021 |
| Contact name |
Micah Gearhart |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Minnesota
|
| Department |
Genetics, Cell Biology and Development
|
| Street address |
6-160 Jackson Hall, 321 Church St.
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL19005 |
| Series (1) |
| GSE161565 |
Profiling NSD3-dependent neural crest gene expression reveals known and novel candidate regulatory factors |
|
| Relations |
| BioSample |
SAMN16810953 |
| SRA |
SRX9515693 |
