|
| Status |
Public on Jun 01, 2018 |
| Title |
embryo_e8_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryo stage e8
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD1
developmental stage: E8.5 (After turning 12-16somites)
tissues: post-occipital region of the embryo
|
| Treatment protocol |
Embryos at similar developmental stages were collected and stored at -80 in RNA later solution
|
| Growth protocol |
Mouse embryos form wild-type CD1 mothers were collected at different days post-coitum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was extracted using the RNAeasy mini kit (Qiagen) following the manufacturer’s instructions. Contaminant DNA was eliminated using the on-column DNAase digestion and RNA was eluted in RNAase free water. RNA was quantified with the Qubit HS RNA quantification kit (Thermo fisher) and the integrity assessed with bioanalyser.
RNA-seq libraries were prepared from 100ng of pure total RNA using the TruSeq Stranded mRNA protocol from Illumina with polyA selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
pool of 2-3 embryos
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.Replicate data set was concatenated together.
Demultiplexed RNA-seq reads were mapped onto the public available GRCm38 (mm10). using TopHat release 2.0.9 (Kim et al., 2013). TopHat output files were processed with SAMTools (Li et al., 2009) and BedTools (Quinlan, 2014) to extract the unique read coverage along the genome. For visualisation and comparison across samples, the read coverage was divided by the number of millions of mapped reads in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of the RNAseq read coverage, divided by the number of millions of mapped reads in each sample.
|
| |
|
| Submission date |
Apr 30, 2018 |
| Last update date |
Jun 01, 2018 |
| Contact name |
Leonardo Beccari |
| E-mail(s) |
leonardo.beccari@unige.ch
|
| Organization name |
University of Geneva
|
| Department |
Genetics and Evolution
|
| Street address |
30 Quai Ernest Ansermet
|
| City |
Geneva |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE106227 |
Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids |
| GSE113885 |
Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids [E6.5 to E9.5] |
|
| Relations |
| BioSample |
SAMN09005546 |
| SRA |
SRX4016355 |
