|
| Status |
Public on Mar 24, 2023 |
| Title |
EpiSC 3 |
| Sample type |
SRA |
| |
|
| Source name |
EpiSC
|
| Organism |
Mus musculus |
| Characteristics |
cell line: EpiSC
treatment: 3 ng/ml FGF2
|
| Treatment protocol |
Mesoderm differentiation of EpiSCs was performed by culture in N2B27 supplemented with 1 µM CHIR99201, 8 ng/ml BMP, and indicated concentrations of FGF2 or AZD4547 for three days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cell transcriptomes were generated with the 10x Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 according to the manufacturer's instructions. Briefly, cells were differentiated for three days, detached with Accutase and counted. The cell suspension was diluted to a concentration of 900 cells/μl, to recover around 2000 cells per sample. Cell suspensions were loaded on a Chromium Controller (10x Genomics) to partition cells with gel beads in emulsion. Reverse transcription, cDNA recovery and amplification, and sequencing library construction were performed according to manufacturer’s instructions (10x Genomics ChromiumNextGEMSingleCell_v3.1_Rev_D). We chose 12 PCR cycles for cDNA amplification, and 10 PCR cycles for index PCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
Demultiplexing, alignment to the mouse genome mm10 (GENCODE vM23/Ensembl 98, from 10x Genomics) and read quantification was performed with CellRanger (10x Genomics, v4.0.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Mar 23, 2023 |
| Last update date |
Mar 24, 2023 |
| Contact name |
Christian Schröter |
| E-mail(s) |
christian.schroeter@mpi-dortmund.mpg.de
|
| Phone |
+492311332223
|
| Organization name |
MPI of Molecular Physiology
|
| Department |
Systemic Cell Biology
|
| Street address |
Otto-Hahn-Str. 11
|
| City |
Dortmund |
| State/province |
Nordrhein-Westfalen |
| ZIP/Postal code |
44227 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE228061 |
Population-level antagonism between FGF and BMP signaling steers mesoderm differentiation in embryonic stem cells |
|
| Relations |
| BioSample |
SAMN33872233 |
| SRA |
SRX19758109 |
