|
| Status |
Public on Mar 09, 2022 |
| Title |
10uM 4oxoRA replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
NF stage 15 embryo
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue/age: Anterior half of NF stage 15 embryo
treatment: 10uM 4-oxo-RA treated
|
| Treatment protocol |
10uM DMSO, 1uM RA or 10uM 4-oxo-RA dilutions were made in 0.1X NAM and anterior halves of Xenopus embryos were treated from NF stage 12.5 to NF stage 15, when they were collected for RNA extraction.
|
| Growth protocol |
WT Xenopus embryos from 3 different femles were cultured in 0.1X NAM. Membranes were removed and anterior halves were dissected at NF stage 12.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Micro kit (Qiagen, Cat# 74004) as per manufacturer’s instructions, including on-column DNase I digestion 15 mins at room temp to eliminate genomic DNA.
Extracted Total RNA from anterior halves of NF stage 15 embryos was verified on the Agilent Bioanalyzer system using a nanochip to verify the RNA integrity number (RIN). High quality total RNA (500ng) was input into the Illumina Truseq v2 stranded mRNA library prep kit (cat#20020595) according to the manufacturer’s protocol. Generated cDNA was amplified with 12 pcr cycles. Final generated libraries were verified on the Agilent Tapestation 2200 system using high sensitivity DNA Screentape. Generated cDNA was amplified with 12 pcr cycles. Final generated libraries were verified on the Agilent Tapestation 2200 system using high sensitivity DNA Screentape. Sample concentration was checked on the Invitrogen qubit system using the high sensitivity DNA reagent. Each sample was normalized to a specific nanomolar concentration and pooled equally into a final combined pool. The pool was run on 1 lane of Novaseq SP100 flow cell (run length was 50 paired end bases) on the Illumina Novaseq 6000 sequencing system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
10uM-4oxoRA_3_S16_L002
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to XENLA_9.2 whole genome using STAR aligner (v2.7.3) following sns rna-star (https://igordot.github.io/sns/routes/rna-star.html) pipeline
Genome_build: XENLA_9.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jul 16, 2021 |
| Last update date |
Mar 09, 2022 |
| 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 |
GPL17682 |
| Series (1) |
| GSE180269 |
Analysis of RA vs 4-oxo-RA gene expression regulation in Xenopus laevis |
|
| Relations |
| BioSample |
SAMN20285871 |
| SRA |
SRX11485387 |
