|
| Status |
Public on Jul 31, 2022 |
| Title |
A single In-utero natural embryo, E8.5, replicate 4 |
| Sample type |
SRA |
| |
|
| Source name |
E8.5 mouse embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: embryo
embryo growth condition: in utero
embryonic day: E8.5
original cells: natural
|
| Treatment protocol |
Doxycycline treatment for sEmbryos.
|
| Growth protocol |
Ex utero culture protocol for sEmbryos. E8.5 in utero control were dissected and used for experiment directly.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted according to 10x Genomics Chromium v3.1 Dual Index system kit instructions.
10x Genomics Chromium v3.1 Dual Index system (5000 cell target cell recovery).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
InUtE85-1emb-r4
A single in-utero natural embryo, E8.5.
Single-cell RNA-seq
|
| Data processing |
Demultiplexing was done with cellranger/3.1.0 mkfastq.
Alignment and quantification of single cell features was done with cellranger counts.
Aggregation of multiple GEM wells was done using- cellranger aggr.
Cells with under 200 expressing genes, over 4000 expressing genes or over 10% mitochondrial gene expression were filtered out for the rest of the analysis.
Assembly: mm10
Supplementary files format and content: Processed data is divided into three different matrices created using Seurat 3.0: raw_counts.csv - contains raw counts of all genes across all cells, normalized_counts.csv - contains normalized counts of all genes across all cells, cell2sample.csv - contains information of each of the cells.
|
| |
|
| Submission date |
Jul 21, 2022 |
| Last update date |
Oct 21, 2022 |
| Contact name |
Noa Novershtern |
| E-mail(s) |
noa.novershtern@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Molecular Genetics
|
| Street address |
Weizmann Institute
|
| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE208680 |
Ex Utero Development of Post-Gastrulation Synthetic-Embryos Generated Solely from Mouse Naïve Pluripotent Stem Cells [scRNA-seq] |
| GSE208681 |
Ex Utero Development of Post-Gastrulation Synthetic Embryos Generated Solely from Naïve Pluripotent Stem Cells |
|
| Relations |
| BioSample |
SAMN29879316 |
| SRA |
SRX17958205 |
