|
Status |
Public on Apr 03, 2021 |
Title |
RNA-seq_WntMo_M2 |
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.
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|
|
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.
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|
|
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 |
SAMN14845425 |
SRA |
SRX8279270 |