|
| Status |
Public on Jun 04, 2019 |
| Title |
Ctx_WT_2 |
| 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 |
| 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 |
SAMN11940074 |
| SRA |
SRX5956914 |
