|
| Status |
Public on Nov 12, 2024 |
| Title |
Whole brain, TNFR1ff, naive, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
whole brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: whole brain
genotype: TNFR1ff
treatment: naïve
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total brain RNA isolation was performed using TRIzol reagent (Thermo Fisher Scientific, T9424) according to the manufacturer’s instructions. RNA purity and quantification were assessed using NanoDrop 2000 spectrophotometer data.
Samples with 381-448 ng of total RNA were processed using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, K01524) for library preparation. The libraries were assessed for molarity and median library size using Bioanalyzer High Sensitivity DNA Analysis (Agilent, 5067-4627).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Quality Control and pre-processing was conducted using FastQC and Cutadapt.
Alignment of the trimmed reads was conducted in a splice-aware manner using the STAR aligner.
Gene-level quantification was performed using RSEM.
Differential expression analysis was conducted using edgeR’s quasi-likelihood negative binomial generalized log-linear model (FDR <0.05).
Assembly: GRCm39
Supplementary files format and content: Unfiltered gene-level quantification results by RSEM (tab-delimited).
|
| |
|
| Submission date |
Sep 26, 2024 |
| Last update date |
Nov 12, 2024 |
| Contact name |
Lesley Probert |
| E-mail(s) |
[email protected]
|
| Organization name |
Hellenic Pasteur Institute
|
| Department |
Immunology
|
| Lab |
Molecular Genetics
|
| Street address |
Vassilisis Sofias 127
|
| City |
Athens |
| State/province |
Attiki |
| ZIP/Postal code |
11521 |
| Country |
Greece |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE278137 |
Microglia regulate cortical remyelination via ΤNFR1-dependent phenotypic polarization [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN43944009 |
| SRA |
SRX26208213 |
