|
| Status |
Public on Nov 23, 2018 |
| Title |
LeeHS201707_XENLAtx_ctrl_1 |
| Sample type |
SRA |
| |
|
| Source name |
LeeHS201707_XENLAtx_ctrl
|
| Organism |
Xenopus laevis |
| Characteristics |
developmental stage: NF stage 32
tissue: whole embryo
|
| Treatment protocol |
For morphants, we injected kdm5c MO and kdm3a MO on two-cell stage embryo.
|
| Growth protocol |
Embryos at NF stage 32 were collected.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The extraction of total RNA was done by lysing the embryos in Isol-RNA lysis reagent (5 Prime, Hamburg, Germany)
RNA sequencing library was constructed according to manufacturer’s instructions (Illumina, San Diego, CA, USA) using polyA enrichment.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
CTRL_1
|
| Data processing |
Mapped paired-reads to primary transcripts with bwa mem (0.7.10)
Filtered out reads mapped on multiple targets (i.e. reads mapped on both species)
Count reads per transcripts, and transferred it to human orthologs (humanized)
Genome_build: X. laevis JGIv18 primary transcripts (available at http://www.xenbase.org)
Supplementary_files_format_and_content: Read counts for each samples based on Xenopus transcripts
|
| |
|
| Submission date |
Jul 26, 2018 |
| Last update date |
Nov 23, 2018 |
| Contact name |
Taejoon Kwon |
| E-mail(s) |
[email protected]
|
| Organization name |
Ulsan National Institute of Science and Technology
|
| Department |
Department of Biomedical Engineering
|
| Street address |
50 Unist-gil
|
| City |
Ulsan |
| ZIP/Postal code |
44919 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL18936 |
| Series (1) |
| GSE117754 |
Critical roles of lysine demethylase Kdm3a in craniofacial and neural development during Xenopus embryogenesis |
|
| Relations |
| BioSample |
SAMN09725318 |
| SRA |
SRX4474418 |
