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Sample GSM2677418 Query DataSets for GSM2677418
Status Public on Dec 23, 2017
Title CN_4
Sample type SRA
 
Source name Optic nerve
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: optic nerve
cell type: astrocyte
disease state: healthy control
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_CN_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 SAMN07260335
SRA SRX2940867

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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