|
| Status |
Public on Feb 19, 2024 |
| Title |
Radiation_PBS_3 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar (Hsd/Cpb:WU)
tissue: brain
Sex: male
cell type: microglia
condition: radiation
treatment: PBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Microglia were isolated using a mechanical tissue dissociation protocol at 4°C as previously described (Galatro et al., 2017). Microglia were sorted by gating the DAPIneg CD11bhigh CD45int cells with FACS. Total RNA was isolated using RNeasy Micro Kit (Qiagen, cat# 74004) according to the manufacturer’s instructions.
Sequencing libraries were generated using the NEBNext Low Input RNA Library Prep Kit for Illumina (New England Biolabs, cat# E6420S/L).
DNA sequencing was performed using a NovaSeq6000 according to the manufacturer's protocols. NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality control was performed using third-party (FastQC v0.11.9) and in-house (FastQA v3.1.27) QC tools.
Adapter trimming and quality filtering was performed with fastp (v0.23.2.)
Alignment with the Ensembl genome Rattus norvegicus (mRatBN7.2) was performed with STAR2 (v2.7.10)
Transcripts were counted with HTSeq (v2.0.2)
Assembly: Ensembl genome Rattus norvegicus (mRatBN7.2)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Apr 18, 2023 |
| Last update date |
Feb 19, 2024 |
| Contact name |
Takuya Oshima |
| E-mail(s) |
t.oshima@umcg.nl
|
| Organization name |
University Medical Center Groningen
|
| Department |
Department of Biomedical Sciences of Cells & Systems
|
| Lab |
Section Molecular Neurobiology
|
| Street address |
Antonius Deusinglaan 1
|
| City |
Groningen |
| State/province |
Groningen |
| ZIP/Postal code |
9713AV |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE229940 |
Radiotherapy induces persistent innate immune reprogramming of microglia into a priming state |
|
| Relations |
| BioSample |
SAMN34233660 |
| SRA |
SRX20000646 |
