|
| Status |
Public on May 31, 2018 |
| Title |
20_8E |
| Sample type |
SRA |
| |
|
| Source name |
Oocyte
|
| Organism |
Xenopus laevis |
| Characteristics |
Stage: Stage 1
biological replicate: 2
position: Vegetal pole
|
| Extracted molecule |
total RNA |
| Extraction protocol |
20 oocytes was mounted to OCT medium and sliced using cryostat. RNA was isolated using TRIzol and reprecipitated by 2.5M Lithium Chloride. 500 ng of total RNA was used for rRNA depletion. Illumina TruSeq RNA Sample Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Ribosomal RNA sequences were removed using sortmerna (version 2) and the SILVA rRNA database (version 119). Low quality reads and adaptor sequences were removed using Trimmomatic PE. Reads were aligned against the reference Xenopus laevis genome using STAR (version 2.4.2a).
Annotated reads were counted using htseq-count with the reference model XL9.1_annot_v1.8.1.primary.gff3
Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT-qPCR experiment.
Genome_build: Xla.v91.repeatMasked.fa (ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.1/)
Supplementary_files_format_and_content: Tab-delimited text files include non-normalized and DESeq2 normalized number of reads for each Sample
|
| |
|
| Submission date |
Oct 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Radek Šindelka |
| Organization name |
Institute of Biotechnology, Czech Academy of Science, v.v.i.
|
| Lab |
Laboratory of Gene Expression
|
| Street address |
Průmyslová 595
|
| City |
Vestec by Prague |
| ZIP/Postal code |
25250 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL17682 |
| Series (1) |
| GSE104848 |
RNA-Seq analysis of localization along animal-vegetal axis of Xenopus laevis |
|
| Relations |
| BioSample |
SAMN07775500 |
| SRA |
SRX3272469 |
