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Sample GSM5254177 Query DataSets for GSM5254177
Status Public on Apr 19, 2024
Title RNAseq Clutch A Sample 4
Sample type SRA
 
Source name Early Embryo
Organism Xenopus tropicalis
Characteristics tissue type: Whole Embryo
developmental stage: Nieuwkoop Faber 10.25
clock time (hours post-fertilization): 7
agent: untreated
Growth protocol Xenopus tropicalis females were injected with 10 units of Chorulon (Merck and Co.) 1-3 nights before embryo collection and 100 units of Chorulon on the day of embryo collection. Eggs were collected in a dish coated with 0.1% BSA in 1/9x MMR. The eggs are in vitro fertilized with sperm suspension in 0.1% BSA in 1/9x MMR. The embryos are dejellied with 3% cysteine in 1/9x MMR, pH 7.8. After 10 minutes, embryos are washed with 1/9x MMR and transferred to 1/9x MMR.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using the acid guanidinium thiocyanate method of Chomczynski and Sacchi (1987: Analytical Biochemistry 162:156-159). Final RNA pellets were resuspended in DEPC-treated water and then precipitated overnight at 4C in 2.5M LiCl to remove contaminating genomic DNA.
Library Construction Protocol: Smart-seq2 cDNA synthesis, Tagmentation
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Paired-end reads were aligned using RSEM v.1.2.12 (Li and Dewey 2011) and Bowtie v2.2.7 (Langmead and Salzberg 2012) to the Xenopus tropicalis genome version 9.0 (Mitros et al., 2019; Karimi et al., 2018). Gene expression in transcripts per million were extracted from RSEM results output.
Genome_build: Xenopus tropicalis v9.0
Supplementary_files_format_and_content: RNA-Seq:The first column is populated by the gene models in the X. tropicalis v9.0 genome annotation. Each subsequent column is the expression of the gene from the 15 RNA-seq datasets.
 
Submission date Apr 20, 2021
Last update date Apr 19, 2024
Contact name Kitt D. Paraiso
E-mail(s) kparaiso@uci.edu
Phone 949-824-7950
Organization name University of California, Irvine
Department Department of Developmental and Cell Biology
Lab Ken W.Y. Cho
Street address 4410 Nat Sci II, University of California, Irvine
City Irvine
State/province CA
ZIP/Postal code 92697
Country USA
 
Platform ID GPL30018
Series (1)
GSE172395 Maternal and zygotic factors sequentially shape the tissue regionalization of chromatin landscapes in early vertebrate embryos
Relations
BioSample SAMN18808512
SRA SRX10641457

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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