|
| Status |
Public on Oct 23, 2022 |
| Title |
Endoderm_St12_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
animal cap
|
| Organism |
Xenopus laevis |
| Characteristics |
treatment: 160 ng/uL activin
developmental stage: Stage12
lineage: Endoderm
|
| Treatment protocol |
see characteristic:treatment in Samples section above
|
| Growth protocol |
population of animal caps were dissected at stage 8.5 and collected at respective stages
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Animal caps were flash frozen in trizol. RNA was harvested using Trizol reagent extraction from Xenopus animal caps. 1ug total RNA was used for construction of sequencing libraries
Illumina TruSeq mRNA-Seq Library Prep Kit- standard protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Read quality evaluated with FastQC
Mapped to X. laevis v9.2 genome downloaded from xenbase using STAR2.6.0
Assembly: X. laevis v9.2
Supplementary files format and content: single csv file of read count for all genes in each sample
|
| |
|
| Submission date |
Mar 14, 2022 |
| Last update date |
Oct 23, 2022 |
| Contact name |
Carole LaBonne |
| E-mail(s) |
clabonne@northwestern.edu
|
| Organization name |
Northwestern University
|
| Department |
Molecular Biosciences
|
| Street address |
2205 Tech Dr
|
| City |
Evanston |
| State/province |
IL |
| ZIP/Postal code |
60208 |
| Country |
USA |
| |
|
| Platform ID |
GPL21248 |
| Series (1) |
| GSE198598 |
Transcriptome sequencing of Xenopus laevis animal caps at six time points in transit from pluripotency to 4 lineages: epidermal, neural, ventral mesoderm and endoderm |
|
| Relations |
| BioSample |
SAMN26658558 |
| SRA |
SRX14462567 |
