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Sample GSM2677993 Query DataSets for GSM2677993
Status Public on Dec 23, 2017
Title 9223Hippo
Sample type SRA
 
Source name Hippocampus
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: hippocampus
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 SAMN07266587
SRA SRX2943301

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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