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Sample GSM6217443 Query DataSets for GSM6217443
Status Public on Apr 05, 2023
Title GM21 fibroblasts, empty vector, biol rep 1, day 8
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 5.746226308
TC01000002.hg.1 4.716559107
TC01000005.hg.1 7.018019935
TC01000006.hg.1 10.56174069
TC01000007.hg.1 10.50437353
TC01000008.hg.1 5.29095506
TC01000010.hg.1 3.508909747
TC01000011.hg.1 5.904187128
TC01000012.hg.1 4.122275925
TC01000013.hg.1 8.201129474
TC01000015.hg.1 4.775490177
TC01000016.hg.1 3.771449158
TC01000017.hg.1 4.962428346
TC01000018.hg.1 7.153984741
TC01000019.hg.1 6.543406848
TC01000020.hg.1 6.728566863
TC01000021.hg.1 6.336661609
TC01000022.hg.1 6.958521301
TC01000023.hg.1 6.708741565
TC01000024.hg.1 7.23121388

Total number of rows: 40888

Table truncated, full table size 1123 Kbytes.




Supplementary file Size Download File type/resource
GSM6217443_rep1_pBABE_D8_HTA-2_0_.CEL.gz 23.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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