|
Status |
Public on Jan 01, 2021 |
Title |
Frog2 Explant Early Neurula |
Sample type |
SRA |
|
|
Source name |
Xenopus explant
|
Organism |
Xenopus laevis |
Characteristics |
developmental stage: Stage 14 tissue: Explanted Tissue age: 16 hours
|
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 |
F2-Explant-EN
|
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 |
SAMN14467219 |
SRA |
SRX8010759 |