|
| Status |
Public on Feb 26, 2024 |
| Title |
St25_null1 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Xenopus tropicalis |
| Characteristics |
tissue: whole embryo
genotype: Sf3b4 null
treatment: n/a
|
| Growth protocol |
Embryos were grown in NAM until desired stage of collection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pools of 5 embryos were used for RNA extraction via the Qiagen Rneasy Micro Kit
Automated stranded RNA-seq library prep, polyA selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
NovaSeq 6000 System (RTA Version 3.4.4)
bcl2Fastq v2.20
Trimming, alignment and generating count matrix were all done by using the sns/rna-star pipeline (https://igordot.github.io/sns/routes/rna-star.html)
Assembly: Xentr10.0 (http://ftp.xenbase.org/pub/Genomics/JGI/Xentr10.0/XENTR_10.0_genome.fasta.gz)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Nov 30, 2023 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Ziyan Lin |
| E-mail(s) |
ziyanlin2352@gmail.com
|
| Organization name |
NYU Grossman School of Medicine
|
| Department |
Applied Bioinformatics Laboratories
|
| Street address |
227 E 30th St.
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL30018 |
| Series (1) |
| GSE249075 |
Sf3b4 mutation in Xenopus tropicalis causes RNA splicing defects and gene dysregulation across development and disrupts cranial neural crest cell migration and survival |
|
| Relations |
| BioSample |
SAMN38526327 |
| SRA |
SRX22700941 |
