|
| Status |
Public on Feb 07, 2018 |
| Title |
Sample_CCE9704 |
| Sample type |
SRA |
| |
|
| Source name |
Cx3cr1CreER:R26-Tomato mice in which all resident macrophages express the endogenous tomato signal while peripheral immune cells do not.
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Olfactory bulb
vsv-infection: Infected
strain: C57BL/6J
cell type: Microglia
phenotypic markers: Ly6G-CD45lowCD11b+Tomato+ cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from FACS-sorted cells stabilized in RNAprotect buffer according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were checked for their quality and consequently trimmed for adaptor sequence and masked for low-quality sequence by using FastQC version 0.11.5 and Trimmomatic version 0.36
Reads were aligned to the GRCm38.87 genome assembly using STAR version 2.5.3a
Counting of reads was performed with htseq-count version 0.9.1
Genome_build: GRCm38.87
Supplementary_files_format_and_content: tab-delimited text files include raw transcript values for each sample
|
| |
|
| Submission date |
Feb 06, 2018 |
| Last update date |
Feb 07, 2018 |
| Contact name |
Marta Joana Costa Jordão |
| Organization name |
Uniklinikum Freiburg
|
| Department |
Neuropathology
|
| Street address |
Breisacher strasse 64
|
| City |
Freiburg |
| ZIP/Postal code |
79106 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15103 |
| Series (1) |
| GSE110188 |
Neuro-glial crosstalk regulates microglia activation and control of viral encephalitis |
|
| Relations |
| BioSample |
SAMN08470230 |
| SRA |
SRX3652426 |
