|
| Status |
Public on Apr 25, 2019 |
| Title |
Sox2_682 |
| Sample type |
SRA |
| |
|
| Source name |
Cerebellar tumor
|
| Organism |
Mus musculus |
| Characteristics |
strain: NSG
tissue: Cerebellar tumor
genotype: Immunodeficient
surface markers: No sorting
|
| Treatment protocol |
No treatment for isolated cells.
|
| Growth protocol |
Primary cerebellar cells and cerebellar tumors were isolated from mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol Reagent (Life Technologies) according to manufacturer’s instructions.
The cDNA libraries were constructed following the standard Illumina protocols by TruSeq RNA and DNA sample preparation kits (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Reads mapping to the reference genome (GRCm38) was performed on quality-checked and trimmed reads using HISAT2. The reference annotation is Ensembl v87.
The overlap of reads with annotation features found in the reference.gtf was calculated using HT-seq v0.6.1. The output computed for each sample (raw read counts) was then used as input for DESeq2 analysis
Genome_build: GRCm38
Supplementary_files_format_and_content: excel file include FPKM values for each samples
|
| |
|
| Submission date |
May 22, 2018 |
| Last update date |
Apr 25, 2019 |
| Contact name |
Yanxin Pei |
| E-mail(s) |
ypei@cnmc.org
|
| Phone |
2024762558
|
| Organization name |
Children's National Medical Center
|
| Department |
Center for Cancer and Immunology
|
| Street address |
111 Michigan Ave NW
|
| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20010 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE114760 |
Remodeling Group 3 medulloblastoma: MYC overexpression alone transforms progenitors of astrocytes and granule neurons in the postnatal cerebellum |
|
| Relations |
| BioSample |
SAMN09237948 |
| SRA |
SRX4112806 |
