|
| Status |
Public on Mar 13, 2024 |
| Title |
HD4 |
| Sample type |
SRA |
| |
|
| Source name |
striatal microglia
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Q175
strain: C57BL/6
Sex: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The striatal microglia from two striata were purified using MACS. After purification, microglia was flash frozen on dry ice, and RNA was harvested using miRNA Micro Kit
RNA sequencing was performed by Genomics Technology Facility, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai using SMART-Seq v4 Ultra Low Input kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired-end reads were aligned to the reference genome using STAR
FeatureCounts was used to count the read numbers mapped per gene
Readcounts were adjusted by TMM normalisation
DESeq2 R package was used to perform differential expression analysis.
P-values were adjusted using Benjamini Hochberg method
Genome_build: Mus musculus Grch38
Supplementary_files_format_and_content: .txt file containing a matrix of genes with readcounts against samples
|
| |
|
| Submission date |
Jan 28, 2022 |
| Last update date |
Mar 13, 2024 |
| Contact name |
Michelle E Ehrlich |
| E-mail(s) |
michelle.ehrlich@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Street address |
1468 Madison Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE195633 |
Analysis of transcriptomic consequences of Tyrobp deletion in a freshly isolated microglia from Huntington's disease mouse model |
|
| Relations |
| BioSample |
SAMN25353162 |
| SRA |
SRX13965933 |
