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Sample GSM3893122 Query DataSets for GSM3893122
Status Public on Jun 17, 2019
Title 3T-R-2_June18: flox transformed cells variant#3 repl2 4-OHT
Sample type SRA
 
Source name Tail Fibroblasts
Organism Mus musculus
Characteristics strain: B6;129s
phenotype: Transformed
tissue: Tail Fibroblasts
treatment: Tamoxifen
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 SAMN12077145
SRA SRX6183299

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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