|
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 |