|
| Status |
Public on Nov 01, 2015 |
| Title |
EZH2OE_normal_lung_1 |
| Sample type |
SRA |
| |
|
| Source name |
Lung tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: normal Lung
genotype: EZH2 overexpression
|
| Growth protocol |
Fresh murine lung tumor nodules were minced and cultured in 100-mm dishes with RPMI-1640/10% FBS/1% penicillin–streptomycin. H661 and H292 cells (obtained from American Type Culture Collection) were cultured in RPMI-1640/10% FBS/1% penicillin–streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent followed by RNA cleanup (Qiagen, #74204).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
EZH2 overexpressing normal lung replicate 1
|
| Data processing |
alignment: TopHat2 using default settings
expression levels: Gene-level expression measurements for 23,021 Ensembl mouse genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. Cufflinks command line-cufflinks --GTF <gtf_file> -q -p 3 -u -b <genome.fa> -o <output directory> <bam_file_from_tophat>
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM files for each sample
|
| |
|
| Submission date |
Jun 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
James Bradner |
| E-mail(s) |
bradner_computation@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Bradner Lab
|
| Street address |
450 Brookline
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE70046 |
Oncogenic deregulation of EZH2 as an opportunity for targeted therapy in lung cancer [RNA-Seq] |
| GSE70047 |
Oncogenic deregulation of EZH2 as an opportunity for targeted therapy in lung cancer |
|
| Relations |
| BioSample |
SAMN03783074 |
| SRA |
SRX1066712 |
