|
| Status |
Public on Sep 15, 2009 |
| Title |
RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Xenopus tropicalis |
| Characteristics |
developmental stage: 10-13 embryo
|
| Growth protocol |
Xenopus tropicalis embryos were obtained from a natural mating procedure after human chorion gonadotropin injection, dejellied in 2% cysteine and collected at the indicated stage.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using Trizol and the Qiagen RNeasy Kit. Subsequently, polyadenylated RNA was selected with the Oligotex mRNA kit (Qiagen) and the mRNA selection was repeated to improve the removal of rRNA. cDNA was prepared with random hexamer primers using Superscript III (Invitrogen) and second strand cDNA was made with DNA polymerase I, DNA ligase and T4 DNA polymerase.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
PolyA selected, reverse transcribed total RNA
Processed_data_file: RNASeq.bed
Processed_data_file: RNASeq_expression_level.txt
Raw data file: 20FDNAAXX_1_sequence.fastq
Raw data file: 20FDNAAXX_4_sequence.fastq
Raw data file: 20FGLAAXX_2_sequence.fastq
Raw data file: 20FDNAAXX_2_sequence.fastq
Raw data file: 20FE3AAXX_8_sequence.fastq
Raw data file: 20FGLAAXX_3_sequence.fastq
Raw data file: 20FDNAAXX_3_sequence.fastq
Raw data file: 20FGLAAXX_1_sequence.fastq
Raw data file: 20FGLAAXX_4_sequence.fastq
Raw file type: fastq
|
| Data processing |
RNA-seq reads were mapped to JGI FilteredModels genes to determine a normalized expression level.
|
| |
|
| Submission date |
Dec 17, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
Gert Jan Veenstra |
| E-mail(s) |
g.veenstra@science.ru.nl
|
| 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 |
GPL9405 |
| Series (1) |
| GSE14025 |
A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos |
|
| Relations |
| SRA |
SRX012313 |
| BioSample |
SAMN00004596 |
