|
| Status |
Public on Nov 24, 2021 |
| Title |
HFD2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryos
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: embryos (8th somite pair to the tail end)
developmental stage: embryonic 9.5 day
treatment: From high-fat diet fed maternal obese mice (MO)
|
| Treatment protocol |
Mouse embryos were dissected and collected on embryonic 9.5 day. After removing the portion of head and first 7 somite pairs, the portion starting from the 8th somite pair till the tail end was collected. For each sample, a total of 15 embryos from three litters of maternal obese (MO) or lean (CT) mice respectively were pooled together for the preparation of cell suspension. One sample for the CT or MO was collected on the same day and repeated on a second day.
|
| Growth protocol |
Female mice were fed with either a control or high-fat diet for 10 weeks before breeding with male mice on a regular chow.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
After mincing, embryo samples were incubated with TryLE Express dissociation reagent (Life Technology) at 37 °C for 15 min, swirled every two minutes, and the reaction was quenched with heat inactivated serum. After washing, the dissociated single-cell suspensions were re-suspended in PBS with 0.04% BSA and filtered through a 40 μm cell strainer.
After checking the viability and counting, single-cell suspensions of each group were loaded onto the Chromium Controller and cDNA libraries were constructed using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 following the manufacturer’s protocol (10X Genomics, Inc.).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
scRNA-seq
|
| Data processing |
Raw sequencing data were pre-processed with Cell Ranger (v3.0.2, 10x Genomics) mapping to the mouse mm10 transcriptome.
Cell transcriptomes were integrated in R using the Seurat package (v3.2.1). Dataset was normalized with a global-scaling normalization method (“LogNormalize”) with default parameters.
Genome_build: mouse mm10 transcriptome (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx
|
| |
|
| Submission date |
May 06, 2021 |
| Last update date |
Nov 24, 2021 |
| Contact name |
Liang Zhao |
| Organization name |
Washington State University
|
| Street address |
100 Dairy Road
|
| City |
PULLMAN |
| State/province |
WA |
| ZIP/Postal code |
99163 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE173994 |
Transcriptomic analysis of E9.5 mouse embryos |
|
| Relations |
| BioSample |
SAMN19044141 |
| SRA |
SRX10808929 |
