|
| Status |
Public on Jan 30, 2021 |
| Title |
mor_vivo_m_B2 |
| Sample type |
SRA |
| |
|
| Source name |
vivo: morula
|
| Organism |
Sus scrofa |
| Characteristics |
developmental stage: Embryo
embryo stage: morula
group: in vivo developed
Sex: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
whole embryo lysis in buffer containing dNTPs and tailed oligo-dT oligonucleotides (30 nt poly-dT stretch and 25 nt universal 5’anchor sequence) plus 3.1 µl PBS
Illumina smart-seq2 according to Picelli et al., (2014)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Porcine_embryos_in_vivo.xlsx
|
| Data processing |
Basic read statistics and read quality was evaluated based on FastQC reports and a MultiQC overview report of all samples was generated.
Adaptors were clipped, sequences shorter than 20 bp were removed, and a low-quality end score of 20 was applied with the Trim Galore! tool
The trimmed reads were aligned against the porcine genome (Sus scrofa 11.1) with HISAT2
The sex of the morulae and hatched blastocysts was assigned based on the expression of DDX3Y, EIF1AY and EIF2S3Y
Differential gene expression analyses was conducted with EdgeR. A false discovery rate (FDR) of < 0.1% and an absolute log2FC > 1 was applied to identify the differentially expressed genes (DEGs)
Genome_build: Sus scrofa 11.1
Supplementary_files_format_and_content: Porcine_embryos_in_vivo.xlsx contains CPM of in vivo developed embryos at the 4-cell, morula and hatched blastocyst stage, including EdgeR DEG analyses results
Supplementary_files_format_and_content: Porcine_embryos_in_vitro.xlsx contains CPM of in vitro produced embryos at the 4-cell, morula and hatched blastocyst stage, including EdgeR DEG analyses results
Supplementary_files_format_and_content: Porcine_embryos_hatched_blastocysts.xlsx contains CPM of in vivo developed and in vitro produced hatched blastocysts, including EdgeR DEG analyses of source-induced differences and sex-specific differences
|
| |
|
| Submission date |
Jul 24, 2020 |
| Last update date |
Jan 30, 2021 |
| Contact name |
Vera van der Weijden |
| Organization name |
Max Planck Institute for Molecular Genetics
|
| Department |
Department of Genome Regulation
|
| Lab |
Sofja Kovaleskaja Research Group Stem Cell Chromatin
|
| Street address |
Ihnestraße 63-73
|
| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26351 |
| Series (1) |
| GSE155043 |
Transcriptome dynamics in early in vivo developing and in vitro produced porcine embryos |
|
| Relations |
| BioSample |
SAMN15638640 |
| SRA |
SRX8817946 |
