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Sample GSM5456948 Query DataSets for GSM5456948
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

Supplementary file Size Download File type/resource
GSM5456948_10uM-4oxoRA_3.txt.gz 239.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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