|
| Status |
Public on Jun 17, 2019 |
| Title |
3T-1_June18: flox transformed cells variant#3 repl1 control |
| Sample type |
SRA |
| |
|
| Source name |
Tail Fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6;129s
phenotype: Transformed
tissue: Tail Fibroblasts
treatment: Untreated
|
| Treatment protocol |
For the excision of Ssrp1 in vitro, primary, immortalized, or transformed cells (1x106) were plated in 150 mm plates. The cells were treated with 2 μM 4-hydroxytamoxifen (4-OHT) for 96 h (primary cells) or 120 h (immortalized and transformed cells). The medium was replaced every 48 h with fresh 2 μM 4-OHT containing medium. The excision of Ssrp1 was confirmed at both the DNA and protein level.
|
| Growth protocol |
For the generation of primary fibroblasts from Ssrp1++lCreERT2+/+, Ssrp1fl/flCreERT2+/+, and Ssrp1fl/+CreERT2+/+ mice, approximately 2 cm piece of the tail tip was collected and digested using 2mg/ml Collagenase A. Isolated cells were maintained in F-12K medium containing 10% FBS and 1% AA. Primary fibroblasts were infected with genetic suppressor element 56 (GSE56) virus and subsequently selected with 500 μg/ml neomycin (G418 Sulfate) to generate immortalized cells. For the generation of transformed fibroblasts, the immortalized fibroblasts were infected with oncogenic H-RASV-12 virus and selected with bleomycin (30 ug/ml). Immortalized and transformed cells were maintained in DMEM medium supplemented with 10% FBS and 1% penicillin-streptomycin. All cells were kept in a sterile humidified tissue culture incubator at 37°C and 5% CO2 for 4 to 5 days to allow cells to adhere to the plate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Monarch® Total RNA Miniprep Kit-T2010S
KAPA RNA HyperPrep with RiboErase
NovaSeq S1 100 PE
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls performed using bcl2fastq v2.20.0.422
RNASeq reads are mapped to mm10 reference genome and refGene annotation database using TopHat 2.1.1
Gene expression quantification is done using featureCounts v1.4.6 with –fracOverlap 1
Genome_build: mm10
Supplementary_files_format_and_content: comma separated file with raw reads count
|
| |
|
| Submission date |
Jun 17, 2019 |
| Last update date |
Jul 14, 2021 |
| Contact name |
Katerina Gurova |
| E-mail(s) |
katerina.gurova@roswellpark.org
|
| Phone |
716-845-4760
|
| Organization name |
Roswell Park Cancer Institute
|
| Department |
Cell Stress Biology
|
| Street address |
Elm and Carlton Str
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14127 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE132695 |
Prevention of chromatin destabilization by FACT is crucial for malignant transformation [gene expression] |
|
| Relations |
| BioSample |
SAMN12077148 |
| SRA |
SRX6183296 |
