|
| Status |
Public on Oct 15, 2020 |
| Title |
Naive Old P9210_158 |
| Sample type |
SRA |
| |
|
| Source name |
Microglia
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
knockout status: ATG7_WT
age: Old
index: `D701-D504 (ATTACTCG-GGCTCTGA)`
|
| Treatment protocol |
Atg7fl/fl Cx3cr1CreERT and Atg7wt/wt Cx3cr1CreERT2 mice were treated with 4mg Tamoxifen three times with 48h intervals to induce recombination. EAE was induced minimum 18 days post Tamoxifen treatment using subcutaneous injections of recombinant mouse myelin oligodendrocyte glycoprotein (rmMOG) aa1-125 and Pertussis toxin i.p.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CNS cells were extracted using Neural Tissue dissociation kit T (Miltenyi Biotech) and sorted using a BD Influx cell sorter. Microglia were sorted as Live, CD11b+ CD45Intermediate(Int) Ly6G- and/or eYFP+. Sorted microglia were lysed in RLT betamercaptoethanol and pooled 1:1 female and male. RNA was prepared using an RNeasy Mini Kit (Qiagen) followed by quality control assessed with a Bioanalyzer 2100 (Agilent). All samples included had high quality RNA (RIN = 8.5–10). RNA was amplified with a SMARTer Stranded Total RNA-Seq Kit–Pico Input Mammalian (Clontech).
RNA libraries were prepared for sequencing using the SMARTer Stranded Total RNA-seq Kit - Pico Input Mammalian (Clontech).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Naive Old
P9210_158
S25
|
| Data processing |
Clustering was done by 'onboard clustering' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using 'HiSeq Rapid SBS Kit v2' chemistry. The Bcl to FastQ conversion was performed using None from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
The Bcl to FastQ conversion was performed using bcl2fastq from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm8 whole genome using STAR in the scilifelab NGI-RNAseq nextlow pipeline
https://github.com/SciLifeLab/NGI-RNAseq
Genome_build: GRCm38
Supplementary_files_format_and_content: ; seperated csv file include Dseq2 normalized counts for every sample
|
| |
|
| Submission date |
Jul 22, 2020 |
| Last update date |
Aug 30, 2020 |
| Contact name |
Ewoud Ewing |
| E-mail(s) |
ewoud.ewing@ki.se
|
| Organization name |
Karolinska Institutet
|
| Department |
Clinical Neuroscience
|
| Street address |
CMM L8:05, Karolinska University Hospital
|
| City |
Stockholm |
| ZIP/Postal code |
SE-171 76 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE154920 |
Transcriptomes of ATG7 Knockout Microglia |
|
| Relations |
| BioSample |
SAMN15607961 |
| SRA |
SRX8796796 |
