|
| Status |
Public on Feb 04, 2022 |
| Title |
uLPS R14143 [104747-001-007] |
| Sample type |
SRA |
| |
|
| Source name |
Primary cultured microglia
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: Subcortical white matter
cell type: Microglia
donor nr: R14143
treatment: 10 µg/mL uLPS
|
| Treatment protocol |
At day 7l,microglia were exposed to 5 µM P2RY6 antagonist (MRS2578) 1hr prior to exposure to uLPS (10 µg/mL), or exposed to uLPS alone. 16 hr after uLPS exposure, mRNA was extracted
|
| Growth protocol |
Microglia were cultured in 1:1 DMEM/HAMF10 medium containing 10% v/v heat inactivated FBS, 2 mM glutamax, 50 units/mL penicillin, 50 µg/mL streptomycin and 10 ng/mL M-CSF. Cells were kept in culture for 8 days without passaging. Half of the medium was replaced by fresh medium containing M-CSF every 3-4 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was isolated using the RNeasy minikit (Qiagen, Cat#74104) according to manufacturer’s protocol
the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Cat#E7420L) was used to prepare and process the samples
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Clustering and sequencing: Illumina NextSeq 6000 was used
Reads were trimmed for adapter sequences using Trimmomatic v0.30
Presumed adapter sequences were removed from the read when the bases matched a sequence in the adapter sequence set (TruSeq adapters) with 2 or less mismatches and an alignment score of at least 12
The Macaca mulatta genomic reference (Macaca_mulatta.Mmul_10.dna.toplevel.fa) was used for alignment of the reads for each sample.
The reads were mapped to the reference sequence using a short read aligner based on Burrows-Wheeler Transform (Tophat v2.0.14) with default settings.
SAMtools v1.3 package was used to sort and index the BAM files. Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq v0.6.1p1.
Genome_build: Macaca_mulatta.Mmul_10.dna.toplevel.fa
Supplementary_files_format_and_content: .count files containing raw gene counts for each sample
Supplementary_files_format_and_content: .tsv files containing FPKM values for each sample
|
| |
|
| Submission date |
Feb 01, 2022 |
| Last update date |
Feb 05, 2022 |
| Contact name |
Raissa Timmerman |
| E-mail(s) |
raissatimmerman@gmail.com
|
| Organization name |
Biomedical Primate Research Centre
|
| Department |
Alternatives
|
| Street address |
Lange Kleiweg 161
|
| City |
Rijswijk |
| ZIP/Postal code |
2288 GJ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL27943 |
| Series (1) |
| GSE195866 |
Microglia P2Y6 receptor signaling regulates a broad range of innate immune responses after TLR engagement |
|
| Relations |
| BioSample |
SAMN25553431 |
| SRA |
SRX14004570 |
