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Status |
Public on Jun 04, 2019 |
Title |
Animal cap ectopic expression Vegt 100 ng, Otx1 100 ng replicate 1 |
Sample type |
SRA |
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|
Source name |
Xenopus tropicalis embryo
|
Organism |
Xenopus tropicalis |
Characteristics |
developmental stage: Stage 10.5 (equivalent) tissue: Animal caps
|
Treatment protocol |
vegt RNA 100 ng & otx1 RNA 100 ng were microinjected into 1-cell stage embryos; animal caps were dissected at stage 9 and RNA was harvested at stage 10.5
|
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, 10 minutes after fertilization and are then ready for manipulation. Embryos were staged using the Nieukwoop-Faber developmental table.
|
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 4°C in 2.5M LiCl to remove contaminating genomic DNA. RNA-seq libraries were generated using Smart-seq2 cDNA synthesis followed by tagmentation, quality-tested using an Agilent Bioanalyzer 2100, quantified using KAPA qPCR and sequenced using Illumina sequencers.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
processed data file: ectopic-expression-vegt,otx1-readcounts.txt processed data file: ectopic-expression-vegt,otx1-TPM.txt
|
Data processing |
RNA-seq gene expression calling: 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 (Hellsten et al., 2010; Xenbase FTP). Read counts and transcripts per million were extracted from RSEM results output. Genome_build: Xenopus tropicalis genome v 9.0
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Submission date |
Aug 02, 2018 |
Last update date |
Jun 04, 2019 |
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 |
GPL23182 |
Series (1) |
GSE118024 |
Endodermal maternal transcription factors establish super enhancers during zygotic genome activation |
|
Relations |
BioSample |
SAMN09760021 |
SRA |
SRX4501209 |