|
| Status |
Public on Jan 14, 2025 |
| Title |
Stim_1 |
| Sample type |
SRA |
| |
|
| Source name |
placenta
|
| Organism |
Mus musculus |
| Characteristics |
tissue: placenta
cell type: placental cell
strain: C57BL/6J
age: 8-10 weeks old
treatment: CPS
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Nuclei were extracted from fresh-frozen placentas using the singulator 100 (S2 Genomics).
Sample 1-4,library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics Chromium Single Cell 3' Reagent Kits
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
|
| |
|
| Submission date |
Jun 27, 2023 |
| Last update date |
Jan 14, 2025 |
| Contact name |
Manami Katoh |
| E-mail(s) |
brainztrust099@gmail.com
|
| Organization name |
The University of Tokyo
|
| Department |
Department of Cardiovascular Medicine
|
| Street address |
7-3-1 Hongo
|
| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8655 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE235916 |
Gene expression profile at single cell level of the placenta from pregnant mice undergoing circadian disruption. |
|
| Relations |
| BioSample |
SAMN35839321 |
| SRA |
SRX20748597 |
