|
| Status |
Public on Jan 30, 2025 |
| Title |
CA218, WT |
| Sample type |
SRA |
| |
|
| Source name |
Hippocampus brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Hippocampus brain
cell type: Whole tissue
treatment: Cardiac arrest induced with potassium chloride
|
| Extracted molecule |
total RNA |
| Extraction protocol |
By using a biopsy punch, fresh-frozen hippocampal brain region from mice were placed into lysis buffer and dounced in pestles to extract the nuclei. Then, the nuclei were washed, incubated on ice, resuspended in buffer and blocked with albumin for being hased using biolegend antibodies. Samples were pooled and loaded onto Chromium single-cell V3 3'chip (10x Genomics)
Nuclei were hashed and pooled and loaded based onto a Chromium single-cell V3 3'chip (10x Genomics) following manufater's protocol for GEM formation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Data were preprocessed with Cell Eanger and reads demultiplexed with DemuxEM. Reads were aligned to mm10 mouse reference genome. Nuclei with genes lower than 350 or genes in less than 10 nulei were removed then we followed Seurat pipeline
Assembly: mm10
Supplementary files format and content: H5ad files with raw counts and logcounts
|
| |
|
| Submission date |
Oct 29, 2024 |
| Last update date |
Jan 30, 2025 |
| Contact name |
Ana B Villasenor Altamirano |
| E-mail(s) |
avillasenoraltamirano@bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital, Harvard Medical School
|
| Department |
Pulmonary and Critical Care
|
| Lab |
Edy Kim Lab
|
| Street address |
60 Fenwood Rd
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE280524 |
Diverse NKT cells regulate early inflammation and neurological outcomes after cardiac arrest and resuscitation |
|
| Relations |
| BioSample |
SAMN44487053 |
| SRA |
SRX26528278 |
