|
| Status |
Public on Feb 04, 2020 |
| Title |
Brain microglia, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
|
| Growth protocol |
All Methods listed in Ydens et al. Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system . Nature Neuroscience. 2019.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All Methods listed in Ydens et al. Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system . Nature Neuroscience. 2019.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
Brain microglia, replicate 3
|
| Data processing |
Image analysis and base calling resulted in .bcl files, which were converted into .fastq files with the CASAVA1.8.2 software.
No Quality Trimming was done.
Star was used for mapping with Star version 2.5.2b and the following command line: STAR --runThreadN 10 --genomeDir XXX --genomeLoad LoadAndKeep --limitBAMsortRAM 20000000000 --readFilesIn SampleFastQs --readFilesCommand zcat --outFileNamePrefix YYY --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --seedSearchStartLmax 30 --outSAMtype BAM SortedByCoordinate
featureCounts v1.5.1 was used for count file generation with the following command line: featureCounts –a GTFFile –G FASTAFile –o OutFile -p -F GTF -g gene_name -t exon -T 10 –largestOverlap
Genome_build: Gencode M11 was used for mapping and counting (mm10)
Supplementary_files_format_and_content: tab-delimited text files including raw counts for each sample
|
| |
|
| Submission date |
Feb 03, 2020 |
| Last update date |
Feb 04, 2020 |
| Contact name |
Liesbet Martens |
| E-mail(s) |
liesbet.martens@irc.vib-ugent.be
|
| Organization name |
VIB-University of Ghent
|
| Department |
VIB Inflammation Research Center
|
| Street address |
Technologiepark 927
|
| City |
Zwijnaarde |
| ZIP/Postal code |
9052 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL15103 |
| Series (2) |
| GSE144705 |
Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system (bulk) |
| GSE144708 |
Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system |
|
| Relations |
| BioSample |
SAMN13977035 |
| SRA |
SRX7668399 |
