|
| Status |
Public on Dec 23, 2017 |
| Title |
42Hippo |
| Sample type |
SRA |
| |
|
| Source name |
Hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: hippocampus
cell type: astrocyte
disease state: healthy control
rip antibody: anti-HA antibody
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spinal cord (Sc), cerebellum (Cb), cerebral cortex (Crx), and hippocampus (Hippo) were collected and snap-frozen by liquid nitrogen. After RNA co-immunoprecipitation process, RNA was isolated using RNeasy MicroKit (Qiagen).
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 NextSeq 500 |
| |
|
| Description |
mRNA co-immunoprecipitated with mouse monoclonal anti-HA antibody
RNA from astrocyte
|
| Data processing |
Data quality check was done on Illumina SAV
Demultiplexing was performed with Illumina CASAVA 1.8.2
The reads were mapped to the latest UCSC transcript set using the ultra fast high-throughput short read aligner Bowtie2 version 2.1.0
Gene expression levels were estimated using RSEM v1.2.15
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes 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 |
GPL19057 |
| Series (2) |
| GSE100329 |
Astrocyte-specific and region-specific transcriptomes in control and EAE mice |
| GSE100330 |
Multiple sclerosis and EAE |
|
| Relations |
| BioSample |
SAMN07266595 |
| SRA |
SRX2943296 |
