|
| Status |
Public on Nov 12, 2013 |
| Title |
Stage6_RiboZero |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Xenopus tropicalis |
| Characteristics |
developmental stage: 6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
X.tropicalis embryos were obtained with in vitro fertilization, dejellied in 3% cysteine and collected at indicated Nieuwkoop-Faber stages. Stage VI oocytes were harvested by treating ovarian follicles with collagenase (Clostridium type I collagenase). Oocytes and embryos from stage 6 - 30 were collected and total RNA was isolated using Trizol and the QIAGEN RNeasy Kit. Subsequently polyadenylated RNA was selected by enriching with the Oligotex mRNA kit (QIAGEN). To ensure complete removal of ribosomal RNA (rRNA), polyadenylated mRNA was subjected to an additional round of Oligotex treatment. Total RNA was subjected to depletion of rRNA using Ribozero Epicentre low input kit.
cDNA was prepared with random hexamer primers using Superscript III (Invitrogen) and the second strand was made with DNA polymerase I, DNA ligase and T4 DNA polymerase. The purified double-stranded cDNA was used for Illumina sample preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Depleted for rRNA with Epicentre Ribo-Zero rRNA removal kit
|
| Data processing |
For RPKM counts reads were aligned to the genome using bwa 0.6.1 and the RPKM was calculated based on JGI 7.2 gene annotation
Genome_build: Xtropicalis_v7
Supplementary_files_format_and_content: The file RPKM.csv contains the genomic location (scaffold, start, end strand) of all genes (JGI 7.2) for the JGI 7.1 genome together with the RPKM values for each gene.
|
| |
|
| Submission date |
Jan 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gert Jan Veenstra |
| E-mail(s) |
[email protected]
|
| Phone |
+31 24 3610541
|
| Organization name |
Radboud University
|
| Department |
Molecular Developmental Biology
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL13741 |
| Series (1) |
| GSE43652 |
A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development |
|
| Relations |
| SRA |
SRX218740 |
| BioSample |
SAMN01893824 |
