|
| Status |
Public on Apr 19, 2024 |
| Title |
RNAseq Clutch A Sample 2 |
| 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 |
SAMN18808514 |
| SRA |
SRX10641455 |
