|
| Status |
Public on Jan 16, 2019 |
| Title |
Mo_2 |
| Sample type |
SRA |
| |
|
| Source name |
Somitic cells
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: somites
Stage: stage 22
strain: J-strain
genotype/variation: etv6 morpholino injected
|
| Treatment protocol |
The somites of stage 22 Xenopus embryos were manually dissected in 0.35x MMR using forceps.
|
| Growth protocol |
Xenopus embryos were obtained by artificial fertilisation. They were cultured at 19 degree in 0.1x MMR (1xMarc’s Modified Ringer: 100 mM NaCl, 2 mM KCl, 1 mM MgCl2, 2 mM CaCl2, 5 mM HEPES, pH 7.5) after being dejellied in 2% cysteine (PH 7.8-8.0).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from somites dissected from 20 WT or etv6-deficient embryos at stage 22. Triple biological replicates were generated.
Indexed libraries were constructed with 1 µg of total RNA using the KAPA Stranded RNA-seq Kit with RoboErase (KK8483) and NEBNext Mutiplex Oligos (NEB#E7500S) for Illumina sequencing, and sequenced using NextSeq 500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw sequence reads were checked for base quality, trimmed and filtered to exclude adapters using Trimmomatic (Version 0.32)
Filtered read were aligned to the X. Laevis V9.1 using STAR with default parameters.
Aligned read features were counted using Subread tool: featureCounts method (version 1.4.5-p1).
Differential gene expression analysis was carried out using EdgR (Bioconductor Package)
An ANOVA-like test analysis was performed between WT and MO samples, using the generalized linear model followed by Estimates “Dispersion”, fitted with “negative binomial model” and estimates “Generalized linear model likelihood ratio”. Genes with a False Discovery Rate (FDR) above 0.05 were filtered out.
Genome_build: Xenopus Laevis V9.1
Supplementary_files_format_and_content: xlsx file contains gene_id, gene_name, RPKM value of each sample, log FC (wt/mo), P value and FDR value.
|
| |
|
| Submission date |
Jun 01, 2018 |
| Last update date |
Jan 16, 2019 |
| Contact name |
Lei Li |
| E-mail(s) |
lei.li@imm.ox.ac.uk
|
| Organization name |
WIMM
|
| Department |
Radcliffe Department of Medicine
|
| Street address |
University of Oxford
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21248 |
| Series (2) |
| GSE115220 |
Etv6-dependent positive and negative gene regulatory network controls vegfa expression in vivo [RNA-seq] |
| GSE115225 |
Etv6-dependent positive and negative gene regulatory network controls vegfa expression in vivo |
|
| Relations |
| BioSample |
SAMN09294203 |
| SRA |
SRX4153295 |
