|
| Status |
Public on Mar 31, 2015 |
| Title |
WT Microgia #2 |
| Sample type |
SRA |
| |
|
| Source name |
Microglia
|
| Organism |
Mus musculus |
| Characteristics |
age: 10-12wk
genotype: Wild type
cell type: Acutely isolated microglia
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were acutely isolated from mouse tissues and sorted via AutoMACS prior to RNA isolation. Qiagen Rneasy mini kit (Cat #74106) was used per manufacturer's protocol for RNA isolation.
RNA-Seq Poly A selection using NEBNext library prep modules
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Wild type microglia, 3 pooled mice 10-12wks old
|
| Data processing |
Basecalls performed using CASAVA
Data were aligned to the mm9 genome using STAR version 2.3.0
Aligned reads were counted against genes from the UCSC mm9 annotation using the htseq-count python library
Data were normalized for library size using the DESeq2 median ratio normalization procedure described in Ander and Huber (2010).
Differential gene expression was assessed using the DESeq2 package in R.
Genome_build: mm9
Supplementary_files_format_and_content: Counts of reads aligning to genes from the mm9 annotation as output from htseq-count
|
| |
|
| Submission date |
Feb 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Turner |
| Organization name |
Signature Science, LLC
|
| Street address |
1670 Discovery Drive
|
| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22911 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE66211 |
Mecp2: an unexpected regulator of macrophage gene expression and function [RNA-Seq] |
| GSE66502 |
Mecp2: an unexpected regulator of macrophage gene expression and function |
|
| Relations |
| BioSample |
SAMN03366538 |
| SRA |
SRX886153 |
