|
| Status |
Public on Aug 17, 2017 |
| Title |
BRAF Senescence Bypass Day 10 Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
BRAF Senescence Bypass Day 10
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Tig3
cell type: diploid embryonic lung fibroblasts
day treament: 10
transduced with: pBabe-puro-BRAFE600 (OIS bypass)
time point: 10days after transduction
|
| Treatment protocol |
Human diploid fibroblast Tig3 cells expressing the ecotropic receptor, hTERT, and the SV40 small T antigen, were transduced with pBabe-puro-BRAFE600 (OIS bypass). The infected population was selected using puromycin 1μg/ml. Ten days after transduction, cells were harvested in Trizol.
Cells were maintained for 9 days after the treatment specified in Treatment
|
| Growth protocol |
Cells were propagated in DMEM (GIBCO) supplemented with 9% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
X2947_6_ST.BRAF_Day_9_R_1_26_7_2014__A_GCCAATA
|
| Data processing |
Reads were demultiplexed using bcl2fastq 1.8.4 with 1 mismatch allowed
Sequencing reads were mapped against the human genome build GRCh37.75 using tophat 2.0.12 with parameters --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were calculated using a custom script that uses the same strategy as HTSeq-count with union mode
Genes that have zero expression across all samples are removed from the dataset.
Genome_build: GRCh37.75
Supplementary_files_format_and_content: The file readcounts.txt contains the absolute gene expressions values for each of the samples.
|
| |
|
| Submission date |
Dec 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Carolyn A de Graaf |
| E-mail(s) |
degraaf@wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute
|
| Street address |
1G Royal Parade
|
| City |
Parkville |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE75643 |
Massive reshaping of genome - nuclear lamina interactions during oncogene induced senescence (RNA-seq) |
| GSE76605 |
Massive reshaping of genome - nuclear lamina interactions during oncogene induced senescence |
|
| Relations |
| BioSample |
SAMN04311861 |
| SRA |
SRX1460273 |
