NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3844069 Query DataSets for GSM3844069
Status Public on Jun 04, 2019
Title Ctx_OE_2
Sample type SRA
 
Source name cortex
Organism Mus musculus
Characteristics genetic background: C57BL/6
strain id: C9orf72
genotype: GFP-PR28 heterozygote
tissue: cortex
age: 6 months
Extracted molecule total RNA
Extraction protocol The cerebellum, cortex and spinal cord of control and heterozygous mice were removed, flash frozen in liquid nitrogen, and total RNA was harvested using Trizol reagent. The library for next-generation sequencing was constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description 6_months_cortex_and_spinal_cord_raw_counts
Data processing FASTQ files were trimmed with Trimmomatic (v0.30) to remove quality of bases lower than 20
clean data were aligned to reference genome (Ensembl, mm10) via software Hisat2 (v2.0.1)
HTSeq (v0.6.1) was used to estimate gene and isoform expression levels from the pair-end clean data
Genome_build: mm10
Supplementary_files_format_and_content: xls format files include raw counts of sequencing reads for each sample
 
Submission date Jun 03, 2019
Last update date Jun 05, 2019
Contact name Zongbing Hao
E-mail(s) zbhao@stu.suda.edu.cn
Organization name Soochow University
Street address 199 Ren-ai Road
City Suzhou
ZIP/Postal code 215123
Country China
 
Platform ID GPL21273
Series (1)
GSE132108 Motor dysfunction and neurodegeneration in a C9orf72 mouse line expressing poly-PR
Relations
BioSample SAMN11940070
SRA SRX5956917

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap