|
| Status |
Public on Dec 23, 2017 |
| Title |
EAE_3 |
| Sample type |
SRA |
| |
|
| Source name |
Optic nerve
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: optic nerve
cell type: astrocyte
disease state: EAE
rip antibody: anti-HA antibody
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Due to the small quantity of tissue, both optic nerves from two mice within each group (EAE or control) were pooled to create each sample. Optic nerves were dissected out and rapidly snap frozen in liquid nitrogen. After RNA co-immunoprecipitation process, RNA was isolated using Direct-zol RNA microPrep (Zymo Research) .
Double-stranded cDNA was generated using a mixture of random hexamers and oligo dT with the Nugen Ovation RNA-Seq System V2 kit and the sequencing library was made using the Kapa LTP library kit.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
mRNA co-immunoprecipitated with mouse monoclonal anti-HA antibody
RNA from astrocyte
mm10.gene_EAE_IP.txt
|
| Data processing |
Data quality check was done on Illumina SAV
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
Qualities of raw sequence data were examined using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and Trimmomatic was used for cleaning.
R package “QuasR” was used for the read alignment to mouse genome (mm10) followed by the counting at gene level.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample
|
| |
|
| Submission date |
Jun 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuichiro Itoh |
| E-mail(s) |
yitoh@ucla.edu
|
| Phone |
3102068999
|
| Organization name |
UCLA
|
| Department |
Neurology
|
| Street address |
635 Charles E. Young Drive South
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE100294 |
Astrocyte-specific and region-specific transcriptomes in control and EAE mice: optic nerve |
| GSE100330 |
Multiple sclerosis and EAE |
|
| Relations |
| BioSample |
SAMN07260340 |
| SRA |
SRX2940870 |
