|
| Status |
Public on Jun 06, 2013 |
| Title |
ESC-FC1801 In Vivo-Treated |
| Sample type |
SRA |
| |
|
| Source name |
ESC-FC1801_in vivo_NXD30001
|
| Organism |
Mus musculus |
| Characteristics |
strain background: FVB/N
genotype/variation: Nf2Flox/Flox, NF2-/- in vitro induced with Ad-Cre
source cell type: mouse embryonic Schwann cells
sample type: ESC-FC1801 cultured cells
treated with: NXD30001 at 100mg/kg, three times a week, for 4 wks
|
| Treatment protocol |
ESC-FC1801 cells in culture were treated with DMSO or 1 uM NXD30001 for 24 hours. Mice bearing an ESC-FC1801 tumor were administered with vehicle or NXD30001 at 100mg/kg, three tims a week, for four weeks.
|
| Growth protocol |
ESC-FC1801 cells were rutinely cultured in serum-free N2 medium (DMEM/F12 with N2 supplement, 10ng/mL Neuregulin-β1, 2uM forskolin , 50ug/mL gentamycin, 1% fungizone).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultured cells and tumor samples were homogenized in Trizol reagent and RNA was isolated using RiboPure total RNA isolation Kit (Ambion). Libraries were prepared using protocol recommended from Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Sample 2
processed data file: gene_exp_diff_Control_NXD30001_fromtophat120_cufflinks102_c0_081612.txt
|
| Data processing |
Bases were called by Casava for GAIIx and by RTA for HiSeq.
Reads were aligned to mm9 genome using TopHat v1.2.0 with parameters -G (using Ensembl NCBI37.58 GTF) and --no-novel-juncs. For the paired end reads, -r 275 was used for control and -r 248 was used for treated.
Transcripts were assembled using Cufflinks v1.0.2. Cuffdiff was used to compare each treated sample to the control sample, using Ensembl NCBI37.58 GTF, and --min-aligment option of 0.
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdif result files include FPKM values for each Sample, as well as q-value and fold change.
|
| |
|
| Submission date |
Aug 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Ascia Eskin |
| Organization name |
UCLA
|
| Department |
Human Genetics
|
| Lab |
Stanley Nelson
|
| Street address |
695 Charles Young Drive South Gonda 5554
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095-7088 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE40187 |
Therapeutic potential of a novel HSP90 Inhibitor, NXD30001, for Neurofibromatosis type 2 |
|
| Relations |
| SRA |
SRX178696 |
| BioSample |
SAMN01120722 |
