|
| Status |
Public on Apr 30, 2020 |
| Title |
NW_ACB2E1_S10_L007 |
| Sample type |
SRA |
| |
|
| Source name |
Noggin+Wnt8 no rRNA depletion, biological rep 2
|
| Organism |
Xenopus laevis |
| Characteristics |
treatment: Noggin+Wnt8 no rRNA depletion
|
| Treatment protocol |
Xenopus laevis embryos were injected at the 2-cell stage with mRNA encoding noggin and wnt8 to induce neural crest progenitors. A subset of these embryos were co-injected with Sf3b4MO antisense oligonucleotides to interfere with neural crest foermation. At the blastula stage (stage 8/9), animal cap explants were dissected and cultured for 8 hours in a defined medium. Three replicate were performed for each condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Individual animal cap explants were homogenized and total RNA extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
NW_no_ribosomedepletion
Animal cap explant dissected from embryo injected with Noggin + Wnt8 mRNAs
|
| Data processing |
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the frog genome (build XL9.2, respectively) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Heatmaps and other statistics was performed using R3.2
Genome_build: XL9_2
Supplementary_files_format_and_content: csv files include raw read counts table for genomic features and Transcript FPKM counts.
|
| |
|
| Submission date |
Jan 09, 2020 |
| Last update date |
Apr 30, 2020 |
| Contact name |
Varshini Vasudevaraja |
| E-mail(s) |
[email protected]
|
| Organization name |
NYU Langone Health
|
| Department |
Pathology
|
| Lab |
Applied Bioinformatics Laboratories
|
| Street address |
550 1st Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL18936 |
| Series (1) |
| GSE143395 |
Targets of Sf3b4 during neural crest development |
|
| Relations |
| BioSample |
SAMN13810625 |
| SRA |
SRX7529447 |
