|
| Status |
Public on May 13, 2016 |
| Title |
RNA_H3.3K36M tumor 3 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor derived from C3H10T1/2 H3.3K36M cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C3H10T1/2
cell type: C3H embryo-derived mesenchymal multipotent cells
genotype: Stably expressing FLAG-HA-tagged K36M mutant H3.3
passages: Not applicable
tissue: tumor derived from C3H10T1/2 H3.3K36M cells
|
| Treatment protocol |
2x10^6 H3.3K36M cells were mixed with Matrigel and injected subcutaneously into both flanks of 6-8 weeks old athymic female SCID mice. Tumors were harvested 5-6 weeks post-injection.
|
| Growth protocol |
C3H10T1/2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, CellGro).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Trizol (Invitrogen).
libraries were prepared according to the Illumina TruSeq protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA_MedianNorm_H31_H33_xenografts
|
| Data processing |
Reads were aligned using bowtie 1.0.0 with default parameters
Expression for annotated refseq genes was determined using RSEM 1.2.12 with default parameters
the data-matrix was normalized by median-normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab separated files containing median normalized 'expected-counts'
|
| |
|
| Submission date |
May 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter W Lewis |
| E-mail(s) |
pwlewis2@wisc.edu
|
| Phone |
608-316-4388
|
| Organization name |
University of Wisconsin-Madison
|
| Department |
Department of Biomolecular Chemistry
|
| Lab |
Room 2174, Wisconsin Institute for Discovery
|
| Street address |
330 N Orchard Street
|
| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53715 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE69285 |
Histone H3K36M mutation impairs mesenchymal differentiation and drives sarcoma development [RNA_H33_K36M_HMT] |
| GSE69291 |
H3K36 mutations promote sarcomagenesis through genome-wide remodeling of H3K36 and H3K27 methylation |
|
| Relations |
| BioSample |
SAMN03737595 |
| SRA |
SRX1040772 |
