|
| Status |
Public on Feb 25, 2021 |
| Title |
ADAM1 |
| Sample type |
SRA |
| |
|
| Source name |
brain immune cells FACS sorted CD45+
|
| Organism |
Mus musculus |
| Characteristics |
strain: APP/PS1 Axl-/- Mertk-/-
tissue: brain
cell type: immune cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Microglia were isolated from 18mo APP/PS1 (AD) and APP/PS1 Axl-/-Mertk-/- (ADAM) cortices, 2 pooled cortices per sample, 2 biological replicates. Briefly, cortices were digested using a combination of enzymatic digestion and mechanical dissociation followed by removal of debris on a Percoll gradient. Single cell preparations were subjected to FACS sorting based on CD45 positivity.
Libraries were prepared according to Illumina's instructions on gene expression library constrcution (CG000204_ChromiumNextGEMSingleCell3_v3.1_Rev_D)
10X Single-Cell RNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned by 10X cell ranger pipeline (v3.1.0) with default setting
Default filtered gene expression matrix was further processed by Seurat (v3.2.1.9002)
Cells with <10% mitochondrial reads and 200-10000 expressed genes were kept in the analysis.
Genome_build: mm10; Ensembl release-93
Supplementary_files_format_and_content: rawCount.tsv contains gene by cell expression raw count matrix
meta_data.tsv contains annotated cell identities and UMAP coordinates
|
| |
|
| Submission date |
Oct 30, 2020 |
| Last update date |
Mar 28, 2022 |
| Contact name |
April Elizabeth Williams |
| E-mail(s) |
apriljack06@gmail.com, awilliams@salk.edu
|
| Phone |
7345461645
|
| Organization name |
Salk Institute for Biological Studies
|
| Department |
IGC
|
| Street address |
10010 N Torrey Pines Rd
|
| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE160523 |
Microglia use TAM receptors to detect and engulf amyloid beta plaques |
|
| Relations |
| BioSample |
SAMN16607231 |
| SRA |
SRX9407200 |
