|
| Status |
Public on Feb 12, 2020 |
| Title |
J3_Acute_Parenchyma_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Acute_Parenchyma
|
| Organism |
Mus musculus |
| Characteristics |
Sex: Female
disease: Acute
region: Parenchyma
molecule subtype: immunoprecipitated mRNA via HA-tagged Rpl22 ribosomal subunit
|
| Treatment protocol |
Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Protocol largely derived from Sanz et al. 2009, PNAS. Each CNS region was microdissected and homogenized in supplemented homogenization buffer (HB-S). Debris was pelleted, and supernatant was immunoprecipitated with an anti-HA antibody (Sigma, #H9658, 1:150) overnight. Following washes, RNA was purifiied using a Qiagen RNeasy purification kit (Qiagen, #74106). mRNA was then isolated using mRNA DIRECT kit (Thermo Fisher, #61012).
Libraries were prepared using a similar protocol as MARS-seq (Jaitin et al. Science 2014).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The right reads were trimmed using fastx (v0.0.13) fastx_trimmer.
Sequencing reads was aligned against the mm10 genome using STAR with default parameters and --quantMode geneCounts to count unique reads mapped
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited gene counts generated from STAR geneCounts
|
| |
|
| Submission date |
Apr 22, 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) |
| GSE130118 |
Genome-wide analysis of the transcriptional profile of astrocytes across EAE by CNS region in Gfap-Cre;Ribotag(f/f) mice uisng Ribotag immunoprecipitation. |
| GSE130119 |
MAFG-driven astrocytes promote CNS inflammation |
|
| Relations |
| BioSample |
SAMN11475543 |
| SRA |
SRX5717465 |
