|
| Status |
Public on Aug 15, 2021 |
| Title |
E1311, Embryo |
| Sample type |
SRA |
| |
|
| Source name |
Embryo
|
| Organism |
Capreolus capreolus |
| Characteristics |
number of embryonic cells: 489
developmental stage: Early diapause
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen AllPrep DNA/RNA Micro Kit
Clonetech pico-input mammalian total RNA kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
E1311.fastq
|
| Data processing |
Trim Galore! for adaptor clipping, removal of sequences shorter than 50 bp and low-quality end score of 30
FastUniq tool for removal of duplicates
Read mapping with Salmon against the roe deer transcriptome
Count table filtering with CPM cut-off of 3.0 and sample cut-off of 5
Differential gene expression with ImpulseDE2
Genome_build: De novo assembled roe deer transcriptome
Supplementary_files_format_and_content: TPM_Embryos.xlsx
|
| |
|
| Submission date |
Sep 30, 2020 |
| Last update date |
Aug 15, 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 |
GPL29202 |
| Series (2) |
| GSE158805 |
Amino acids activate mTORC1 to release roe deer embryos from decelerated proliferation during diapause [Embryo] |
| GSE158806 |
Amino acids activate mTORC1 to release roe deer embryos from decelerated proliferation during diapause |
|
| Relations |
| BioSample |
SAMN16303712 |
| SRA |
SRX9219720 |
