|
| Status |
Public on Mar 15, 2022 |
| Title |
HU_NT_1 |
| Sample type |
SRA |
| |
|
| Source name |
Nuclear transferred embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain: BDF1
treatment: hydroxyurea treated
tissue: embryo
|
| Treatment protocol |
Embryos were then randomly distributed in medium with or without HU (10uM), which was replaced by fresh medium without HU after 24 h.
|
| Growth protocol |
MII oocytes were collected and enucleated in CZB medium and were then let to recover in KSOM until they were used for nuclear transfer. The nuclei of donor cumulus cells were injected into the enucleated oocytes using a Piezo-driven micromanipulator. After reconstruction, oocytes were cultured for 1 h in KSOM and activated for 6 h in KSOM containing 10 mM Sr2+ and 5 ug/ml CB supplemented with 2 mM EGTA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Individual cells were manually picked into the lysis solution with macrocapilary pipettes and cDNA was synthesized acording to the Smart-seq2 protocol. Quality of cDNA was checked by the bioanalyzer both after and before the tagmentation.
Libraries were prepared with Smart-seq2 protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quality control of the sequencing was analyzed with FastQC
Demultiplexed reads were aligned using STAR (version 2.7.3a) with the default parameters, the gene counts were produced with the same command using the option “--quantMode GeneCounts”. The annotation used was downloaded from iGenomes (UCSC as the source), the ERCC genes and mitochondrial genes (from ENSEMBL) were added to the annotation for quality control metrics.
Using unix commands, a count matrix was created by joining the individual count files produced by STAR
The count matrix was processed with custom R (version 4.0.2) scripts. The scripts were used for the quality control, cleaning of the matrix, and principal component analyses
Genome_build: mm10
Supplementary_files_format_and_content: Txt, named counts and FPKM table ready to load in R with rows as genes, and columns as samples
|
| |
|
| Submission date |
Feb 08, 2021 |
| Last update date |
Mar 15, 2022 |
| Contact name |
Maria Elena Torres-Padilla |
| E-mail(s) |
torres-padilla@helmholtz-muenchen.de
|
| Organization name |
Helmholtz Zentrum München
|
| Department |
Institute of Epigenetics and Stem Cells
|
| Street address |
Feodor-Lynen-Strasse 21
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE166338 |
Single embryo RNA-seq of control and hydroxyurea treated embryos produced by nuclear transfer of cumulus cells. Single cell RNAseq of cumulus cells was performed using the same protocol. |
|
| Relations |
| BioSample |
SAMN17833434 |
| SRA |
SRX10046872 |
