|
| Status |
Public on Jun 23, 2021 |
| Title |
Pre_activin_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Pre_activin
|
| Organism |
Xenopus laevis |
| Characteristics |
genotype: wild type
Stage: mid-blastula stage embryos (stage 8.5)
tissue: animal cap
treatment: untreated control (Pre_activin)
|
| Treatment protocol |
Dissected animal caps were cultured in activin A solution (50 ng/mL in Steinberg's solution containing 0.1% BSA and 0.1 mg/mL kanamycin sulfate) for 1, 3, 6 and 9 hours at 18℃. As a negative control, animal caps were collected immediately after dissection in the absence of activin A treatment.
|
| Growth protocol |
Xenopus laevis embryos were cultured in Steinberg's solution, and animal caps were removed from mid-blastula stage embryos (stage 8.5) with forceps and tungsten needles.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10 animal caps per sample, in triplicate, were homogenized into ISOGEN (Nippon Gene) at 25℃. Total RNA was extracted according to the manufacture's protocol. Extracted total RNA was purified by using Rneasy Mini kit (QIAGEN), and eluted RNA was mixed with 2.5 volume iced ethanol and NaCl (final concentration, 33mM) for ethanol precipitation. Precipitated RNA was centrifuged at 4℃ for 30 minutes. After removal of supernatants, RNA pellets were washed with 80% ethanol. RNA pellets were dried up and resuspended with RNase free water.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped to the X. laevis v9. 2 genome (Xenbase) and quantified using CLC Genomics Workbench version 12.0 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.
Genome_build: X. laevis v9.2
Supplementary_files_format_and_content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.
|
| |
|
| Submission date |
Jul 07, 2020 |
| Last update date |
Jun 23, 2021 |
| Contact name |
Jun-Dal Kim |
| Organization name |
University of Toyama
|
| Department |
Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)
|
| Lab |
Complex Biosystem Research Lab.
|
| Street address |
2630 Sugitani
|
| City |
Toyama |
| State/province |
Toyama |
| ZIP/Postal code |
930-0194 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21248 |
| Series (1) |
| GSE153925 |
Comprehensive expression profile reveals dynamic changes in Xenopus gene expression depending on the duration of activin A treatment. |
|
| Relations |
| BioSample |
SAMN15463432 |
| SRA |
SRX8678466 |
