|
| Status |
Public on Apr 03, 2021 |
| Title |
RNA-seq_WntMo_M3 |
| Sample type |
SRA |
| |
|
| Source name |
Single neural fold
|
| Organism |
Gallus gallus |
| Characteristics |
developmental stage: HH9
genotype: Wnt knockdown
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Loss of function assays were performed after bilateral injections with their respective controls. Wnt knockdown was performed by the combined inhibition of Wnt 1 and 4 by morpholinos. For RNA expression levels, paired single neural folds were finely dissected and total RNA isolated with the RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher Scientific, #AM1931) according to the kit’s protocol.
RNA was poly(A) selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490). TruSeq-barcoded RNAseq libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760) and sequenced on an Illumina NextSeq500 instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq of neural upon Wnt knockdown
|
| Data processing |
Reads were trimmed using CutAdapt, and aligned to the galGal5 genome using hisat2 and quantified using featureCounts on genes from ENSEMBL release 93. Gene counts were processed using in R and differentially expressed genes were called using DESeq2. Lowly-expressed genes were removed (less than 5 counts any two samples) and DESeq2 revealed 254 differentially expressed genes (padj < 0.05). Regularized logarithm counts were exported for additional analysis.
|
| |
|
| Submission date |
May 06, 2020 |
| Last update date |
Apr 03, 2021 |
| Contact name |
Marcos Simoes-Costa |
| E-mail(s) |
simoescosta@cornell.edu
|
| Organization name |
Cornell University
|
| Department |
Molecular Biology and Genetics
|
| Lab |
Simoes-Costa Lab
|
| Street address |
526 Campus Rd
|
| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL19787 |
| Series (1) |
| GSE150006 |
The connectome of neural crest enhancers reveals regulatory features of signaling systems |
|
| Relations |
| BioSample |
SAMN14845423 |
| SRA |
SRX8279272 |
