|
| Status |
Public on Sep 27, 2022 |
| Title |
XENLA_scCapSt12 |
| Sample type |
SRA |
| |
|
| Source name |
NF Stage 12 Animal Cap
|
| Organism |
Xenopus laevis |
| Characteristics |
developmental stage: NF stage 12
|
| Treatment protocol |
No treatment (wild-type)
|
| Growth protocol |
We maintained the animal cap explant under MMR buffer.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
We followed the standard 10X Genomics 3'-seq protocol, and sequenced it with Illumina NextSeq 550.
10X single cell 3'-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
We downloaded the genome of Xenopus laevis from XenBase (RRID: SCR_003280; also available at NCBI GenBank accession number GCA_001663975.1).
We used the annotation from the GitLab repository (https://gitlab.com/Xenbase/genomics/XENLA_9.2; 2018-May version) which is also maintained by the XenBase.
We mapped our raw sequencing data against this database using the CellRanger (version 2.1.1) with the default option for 3’ Gene Expression v2 Libraries (‘SC3Pv2’).
Genome_build: xenLae2 (X. laevis genome 9.2)
Supplementary_files_format_and_content: cellranger_output
|
| |
|
| Submission date |
Sep 16, 2020 |
| Last update date |
Sep 27, 2022 |
| Contact name |
Taejoon Kwon |
| E-mail(s) |
tkwon@unist.ac.kr
|
| 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 |
GPL25291 |
| Series (1) |
| GSE158088 |
Development of Xenopus Mucociliary Epithelium |
|
| Relations |
| BioSample |
SAMN16186887 |
| SRA |
SRX9137551 |
