|
| Status |
Public on Jan 01, 2021 |
| Title |
Frog3 Explant 8Cell |
| Sample type |
SRA |
| |
|
| Source name |
Xenopus explant
|
| Organism |
Xenopus laevis |
| Characteristics |
developmental stage: Stage 4
tissue: Explanted Tissue
age: 2 hours 15 mins
|
| Extracted molecule |
total RNA |
| Extraction protocol |
D1 blastomere was either injected with fluorescent dye or explanted away from the developing embryo.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
F3-Explant-8Cell
|
| Data processing |
Illumina Real Time Analysis (RTA) v2 was used for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Xla.v91 genome and .gff3 file using Tophat/bowtie2
Fragments Per Kilobase Million (FPKM) were calculated and differentially compared using Cufflinks/Cuffdiff. FPKMs were also converted in Transcripts Per Million (TPM)
Genome_build: bowtie2 Xla.v91.fa
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Mar 27, 2020 |
| Last update date |
Jan 01, 2021 |
| Contact name |
Paul Huber |
| E-mail(s) |
phuber@nd.edu
|
| Organization name |
University of Notre Dame
|
| Department |
Chemistry & Biochemistry
|
| Street address |
251 Nieuwland Science Hall
|
| City |
Notre Dame |
| State/province |
Indiana |
| ZIP/Postal code |
46556 |
| Country |
USA |
| |
|
| Platform ID |
GPL21248 |
| Series (1) |
| GSE147621 |
Proteomic and Transcriptomic Analysis of Neural Cell Fate in Developing Xenopus laevis Embryos and Explants |
|
| Relations |
| BioSample |
SAMN14467233 |
| SRA |
SRX8010745 |
