|
| Status |
Public on Feb 12, 2020 |
| Title |
Nrf_KD_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Nrf_KD_flow cytometry sorted astrocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57Bl/6
genotype/variation: sgNfe2l2-targeted
Sex: male
age: P84
cell type: Flow cytometry sorted astrocytes
|
| Treatment protocol |
Induction of EAE in mice. EAE was induced by injecting 25 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared by the Broad Institute according to Smart-seq 2 protocol as described (Picelli et al., 2014)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
*_HMW5KBGX9.*.GTAGAGGA_AGAGGATA
|
| Data processing |
Reads were aligned against the GRCm38 mouse genome using STAR (v.2.5.3) with parameters --twopassMode Basic --alignIntronMax 1000000 --sjdbOverhang 37 --alignMatesGapMax 1000000
Reads were marked for duplicates using Picard (v.2.7.1)
Reads were removed for duplicates, mapping quality below 30, unmapped reads, mate unmapped, and multi-mapped.
Reads were counted using FeatureCounts from Subread (1.5.0) in pair-end mode
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file containing Gene IDs and number of reads mapping to that gene
|
| |
|
| Submission date |
Apr 13, 2019 |
| Last update date |
Feb 12, 2020 |
| Contact name |
Michael Wheeler |
| E-mail(s) |
mwheeler0@bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital
|
| Department |
Neurology
|
| Street address |
60 Fenwood Rd.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE129774 |
Genome-wide analysis of the transcriptional profile of WT and Nfe2l2 KD astrocytes during EAE in B6 mice [Nrf2 RNA-seq] |
| GSE130119 |
MAFG-driven astrocytes promote CNS inflammation |
|
| Relations |
| BioSample |
SAMN11413286 |
| SRA |
SRX5679306 |
