|
| Status |
Public on Aug 22, 2016 |
| Title |
ac1 |
| Sample type |
SRA |
| |
|
| Source name |
embryo_animal cap
|
| Organism |
Xenopus tropicalis |
| Characteristics |
developmental stage: Early gastrula stage (N&F stage 10-10.25)
embryo region: animal cap
illumina rna-seq bar codes: TGACCA
|
| Treatment protocol |
Early gastrula stage (N&F stage 10-10.25) Xenopus tropicalis embryos were dissected into dorsal, lateral and ventral marginal zones, animal caps and vegetal masses. Pooled explants (~30 explants for each region except lateral marginal zones, which used double this number due to 2 lateral explants per embryos) were used to generate RNA for libraries.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using the acid guanidinium thiocyanate method of Chomczynski and Sacchi (1987: Analytical Biochemistry 162:156-159). Final RNA pellets were resuspended in DEPC-treated water and then precipitated overnight at 4oC in 2.5M LiCl to remove contaminating genomic DNA). Agilent Bioanalyzer analysis revealed all RIN scores to be above 9.
The Illumina TruSeq kit was used to isolate polyA+ RNA and construct non-stranded libraries. All cleanup steps used Ampure XP beads. Library quality was assessed by Agilent Bioanalyzer and KAPA qPCR, they were multiplex sequenced and bar-codes on Illumina adaptors were used for de-multiplexing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNAseq reads were aligned using RSEM v1.2.12 using default parameters. RSEM returned the RNA expression from each gene model in both read counts and transcripts per million.
Genome_build: Xenopus tropicalis version 9.0
Supplementary_files_format_and_content: rsem_v9_counts.txt contains the RNA expression in the number of reads that aligned to the gene models in all 12 RNAseq samples. Each row in the file is a gene model and each column is the RNA expression. The file is tab-delimited.
Supplementary_files_format_and_content: rsem_v9_tpm.txt contains the RNA expression in transcripts per million in all 12 RNAseq samples. Each row in the file is a gene model and each column is the RNA expression. The file is tab-delimited.
|
| |
|
| Submission date |
May 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kitt D. Paraiso |
| E-mail(s) |
kparaiso@uci.edu
|
| Phone |
949-824-7950
|
| Organization name |
University of California, Irvine
|
| Department |
Department of Developmental and Cell Biology
|
| Lab |
Ken W.Y. Cho
|
| Street address |
4410 Nat Sci II, University of California, Irvine
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL21874 |
| Series (1) |
| GSE81458 |
Regional expression of X. tropicalis transcription factors in early gastrula embryos |
|
| Relations |
| BioSample |
SAMN05001349 |
| SRA |
SRX1763440 |
