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Sample GSM6217469 Query DataSets for GSM6217469
Status Public on Apr 05, 2023
Title GM21 fibroblasts, RAS, biol rep 3, day 13
Sample type RNA
Source name GM21 fibroblasts at day 13 post-transduction with H-RAS-G12V
Organism Homo sapiens
Characteristics cell type: skin fibroblast
Treatment protocol GM21-RASV12 fibroblasts and their empty vector counterparts were generated by retroviral transduction. GM21 fibroblasts constitutively expressing non-targeting and POU2F2-targeting shRNAs (pLKO.1-Neo-CMV-tGFP, pLKO.1-Neo-CMV-tGFP-TRCN0000245324 and pLKO.1-Neo-CMV-tGFP-TRCN0000245325) (Millipore-Sigma, Saint Louis, MO) were generated by lentiviral transduction and selected with 400 µg/ml neomycin for seven days. Cells were subsequently retrovirally transduced with RASV12
Growth protocol Human somatic GM21 foreskin fibroblasts (Coriell Institute, Camden, NJ) and WI-38 human fetal lung fibroblasts (European Collection of Authenticated Cell Cultures, Porton Down, UK) were cultured in a DMEM medium containing 10% fetal bovine serum (FBS) and 1× penicillin/streptomycin (Corning) at 37 °C in a 2% oxygen atmosphere
Extracted molecule total RNA
Extraction protocol Macherey-Nagel RNA XS columns. At least 200 ng RNA with RIN number 9 were used for library construction.
Label biotin
Label protocol Fragmented and labeled DNA targets were prepared according to the standard Affymetrix WT PLUS Reagent Kit protocol from 100 ng total RNA starting material and 5.5 µg single strand cDNA.
Hybridization protocol Hybridization cocktail of fragmented and labeled ss-cDNA were incubated 16hr, 60rpm at 45°C on Human Transcriptome Arrays 2.0. Genechips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip® Expression Wash, Stain, and Scan User Manual for Cartridge Arrays (PN 702731)
Scan protocol GeneChips were scanned using the Affymetrix GCS 3000 scanner.
Description Gene expression profiling of the entry and exit from RAS-induced senescence in GM21 fibroblasts
Data processing Raw Affymetrix HTA 2.0 array intensity data were analyzed using open-source Bioconductor packages on R. All the data were normalized all together using the robust multi-array average normalization approach implemented in the oligo package (Carvalho and Irizarry, 2010). Internal control probe sets were removed and average expression deciles over all treatment and time points. Probes whose average expression was lower than the 4th expression decile were removed for subsequent analyses.
To remove sources of experimental variation and consider batch effects, data were finally corrected with the sva package. Principal component analysis and bi-clustering based on Pearson’s correlation and Ward’s aggregation criterion were used to confirm consistency between biological replicates and experimental conditions at each step of the pre-processing.
Submission date Jun 08, 2022
Last update date Apr 06, 2023
Contact name Ricardo Iván Martínez Zamudio
Organization name Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School
Department Pharmacology
Lab Martínez Zamudio Lab
Street address 675 Hoes Lane West
City Piscataway
State/province New Jersey
ZIP/Postal code 08854
Country USA
Platform ID GPL17586
Series (2)
GSE205692 Escape From Oncogene-Induced Senescence is Controlled by POU2F2 and Memorized by Chromatin Scars [Expression]
GSE206496 Escape From Oncogene-Induced Senescence is Controlled by POU2F2 and Memorized by Chromatin Scars

Data table header descriptions

Data table
TC01000001.hg.1 5.929414169
TC01000002.hg.1 4.79336331
TC01000005.hg.1 7.588954151
TC01000006.hg.1 11.02867284
TC01000007.hg.1 11.1230902
TC01000008.hg.1 5.435930684
TC01000010.hg.1 3.139723798
TC01000011.hg.1 6.045665383
TC01000012.hg.1 3.700601
TC01000013.hg.1 9.59948829
TC01000015.hg.1 4.91913946
TC01000016.hg.1 4.945489148
TC01000017.hg.1 4.449526234
TC01000018.hg.1 7.36658678
TC01000019.hg.1 6.456799792
TC01000020.hg.1 6.572877055
TC01000021.hg.1 6.261762716
TC01000022.hg.1 7.154253948
TC01000023.hg.1 6.345529103
TC01000024.hg.1 7.060414068

Total number of rows: 40888

Table truncated, full table size 1124 Kbytes.

Supplementary file Size Download File type/resource
GSM6217469_rep3_RAS_D13_HTA-2_0_.CEL.gz 23.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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