|
Status |
Public on May 13, 2016 |
Title |
RNA_siRNA_HMT 1 |
Sample type |
SRA |
|
|
Source name |
C3H10T1/2 cells
|
Organism |
Mus musculus |
Characteristics |
cell line: C3H10T1/2 cell type: C3H embryo-derived mesenchymal multipotent cells genotype: Parental Cells treated with siRNAs against Nsd1, Nsd2 and Setd2 passages: Passage 10-15
|
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_wt_K36M-siRNA-control
|
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 |
SAMN03737590 |
SRA |
SRX1040767 |