|
Status |
Public on Dec 23, 2017 |
Title |
9496HA |
Sample type |
SRA |
|
|
Source name |
Spinal cord
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: spinal cord cell type: astrocyte disease state: EAE 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 |
SAMN07266614 |
SRA |
SRX2943274 |