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Sample GSM3844067 Query DataSets for GSM3844067
Status Public on Jun 04, 2019
Title Ctx_WT_3
Sample type SRA
Source name cortex
Organism Mus musculus
Characteristics genetic background: C57BL/6
strain id: C9orf72
genotype: WT
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
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
BioSample SAMN11940072
SRA SRX5956915

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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