|
| Status |
Public on Oct 06, 2024 |
| Title |
Microlgia, Male 1 wk Control, sample 1 |
| Sample type |
SRA |
| |
|
| Source name |
Brain, cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Brain, cortex
cell type: Microglia
genotype: C57BL/6J
treatment: Male Control
|
| Treatment protocol |
Mice were treated for 1 week prior to microglia isolation with PLX3397 or control chow.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Microglia were isolated using FACS. Total microglial RNA was extracted using the RNeasy Plus Micro Kit (Qiagen). RNA concentration was determined with the NanopDrop One spectrophotometer (NanoDrop) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent). 500 pg of total RNA was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Fluorometer 3.0 (Life Technnologies) and the Agilent Bioanalyzer 2100 (Agilent).
150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina) per manufacturer’s protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
11C
|
| Data processing |
Raw reads generated from the Illumina basecalls were demultiplexed using bcl2fastq v2.19.1
Quality filtering and adapter removal was performed using FastP v.0.23.1.
Processed reads were then mapped to the mouse reference genome (GRCm39 + gencode-M31 annotation) using STAR_2.7.9a.
Read counts were quantified using both Subread-featureCounts v2.0.1 with “-s 0” indicating unstranded reads, and Salmon v1.5.2.
Assembly: GRCm39
Supplementary files format and content: tab delimited text file includes normalized counts for each sample.
Supplementary files format and content: The tximport package was used to import and summarize Salmon transcript-level abundance, estimated counts and transcript lengths into gene-level counts, which were then normalized.
|
| |
|
| Submission date |
Oct 05, 2024 |
| Last update date |
Oct 06, 2024 |
| Contact name |
Ania K. Majewska |
| E-mail(s) |
Ania_Majewska@urmc.rochester.edu
|
| Organization name |
University of Rochester Medical Center
|
| Department |
Department of Neuroscience
|
| Street address |
601 Elmwood Ave
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE278897 |
The microglial response to inhibition of Colony-Stimulating-Factor-1 Receptor by PLX3397 differs by sex in adult mice |
|
| Relations |
| BioSample |
SAMN44073148 |
| SRA |
SRX26297532 |
