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Sample GSM6217439 Query DataSets for GSM6217439
Status Public on Apr 05, 2023
Title GM21 fibroblasts, empty vector, biol rep 1, day 56
Sample type RNA
 
Source name GM21 fibroblasts empty vector time-alone control at day 56 post-transduction
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 time alone 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 Utz Herbig
E-mail(s) herbigut@njms.rutgers.edu
Organization name Rutgers Biomedical and Health Sciences|Rutgers University
Department Center for Cell Signaling|Rutgers‐New Jersey Medical School
Street address 205 South Orange Avenue
City Newark
State/province New Jersey
ZIP/Postal code 07103
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
ID_REF
VALUE RMA

Data table
ID_REF VALUE
TC01000001.hg.1 5.970082301
TC01000002.hg.1 5.011677981
TC01000005.hg.1 7.603001832
TC01000006.hg.1 11.29159188
TC01000007.hg.1 11.18656525
TC01000008.hg.1 5.213361603
TC01000010.hg.1 4.159781326
TC01000011.hg.1 5.676804958
TC01000012.hg.1 4.391010136
TC01000013.hg.1 9.170697484
TC01000015.hg.1 4.930126712
TC01000016.hg.1 4.516721382
TC01000017.hg.1 5.017291674
TC01000018.hg.1 6.992449144
TC01000019.hg.1 6.717879009
TC01000020.hg.1 6.801751168
TC01000021.hg.1 6.449514066
TC01000022.hg.1 7.042816396
TC01000023.hg.1 6.764950578
TC01000024.hg.1 7.421637383

Total number of rows: 40888

Table truncated, full table size 1124 Kbytes.




Supplementary file Size Download File type/resource
GSM6217439_rep1_pBABE_D56_HTA-2_0_.CEL.gz 22.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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