|
| Status |
Public on Feb 12, 2020 |
| Title |
EAE_rep1 [D11] |
| Sample type |
SRA |
| |
|
| Source name |
EAE mouse
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
genotype/variation: wild type
Sex: Male
age: P90
treatment: experimental autoimmune encephalomyelitis (EAE)
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. ICV injection of 100 ng IL-1b and 50 ng TNFa. Cells were isolated 24 hours post-injection of IL1b/TNFa
|
| 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 the 3' DGE protocol as described (Soumillon et al., bioRxiv 2014)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
D11.CGACTT
|
| Data processing |
DGE libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform.
Reads were first demulitplex using Picard (v.2.17.11) IlluminaBaseCallsToSam.
Reads were aligned using GRCh38 mouse genome with STAR (v2.4.2a) with default parameters
Duplicate reads are marked with Picard UmiAwareMarkDuplicatesWithMateCigar to identify duplicate reads based on UMI sequence and alignment start site.
Gene are then quantified using RSEM v1.2.21 with paired-end option and accessed for quality using RNA-SeQC.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt format with gene ID, symbol, and RPKM
|
| |
|
| Submission date |
Sep 12, 2019 |
| Last update date |
Feb 13, 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) |
| GSE130119 |
MAFG-driven astrocytes promote CNS inflammation |
| GSE137314 |
Genome-wide analysis of the transcriptional profile of IL1b/TNFa-treated and EAE astrocytes in B6 mice. |
|
| Relations |
| BioSample |
SAMN12735802 |
| SRA |
SRX6835069 |
