|
| Status |
Public on Jun 01, 2024 |
| Title |
E7.5 embryo YT_E7-5-1_S3_L002 |
| Sample type |
SRA |
| |
|
| Source name |
E7.5 embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: embryonic tissue
strain: C57BL/6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos were harvested from the uterus and dissected in cold dissecting buffer (Dulbecco’s phosphate buffered saline with 10% fetal bovine serum and antibiotics). Dissected tissues were dissociated in 0.125% collagenase type I (Sigma-Aldrich) and 1 U Dispase (Stemcell Technologies) at 37°C for 30 min. The samples were reduced to single cell suspension by tripsin digestion, washed with cold PBS, and passed through 40mm cell strainer.
Embryonic cells were lysed and single cell libraries prepared by following protocols provided by 10x Genomics. For the ESC differentiation experiment, we utilized the MULTI-seq sample barcoding and library preparation protocol from the McGinnis lab (McGinnis et al. 2019).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
E7.5 embryo
embryo_filtered.loom
|
| Data processing |
10X CellRanger was used for the preprocessing of all the FASTQ files.
Genome_build: GRCm38
|
| |
|
| Submission date |
Jun 22, 2021 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Patrick Cahan |
| Organization name |
Johns Hopkins University
|
| Lab |
Cahan lab
|
| Street address |
733 North Broadway, MRB 653
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE178686 |
Quantitative comparison of in vitro and in vivo embryogenesis at a single cell resolution |
|
| Relations |
| BioSample |
SAMN19814158 |
| SRA |
SRX11198773 |
