NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2177041 Query DataSets for GSM2177041
Status Public on Aug 30, 2017
Title MRC5 fibroblasts, day 5, replicate 2
Sample type RNA
 
Source name MRC5 fibroblasts, day 5
Organism Homo sapiens
Characteristics gender: male
cell line: MRC5 cells (ATCC Ca # CCL-171, Lot 59474707) of passages 7-10.
protocol: mock infection
time: five days following mock infection
Treatment protocol On day 0, about 1-1.2 x 10^5 cells grown on 6-well plates were infected with a combination of lentiviruses separately encoding O,S,K and M (OSKM samples) or O, S(v), K and M (OS(v)KM samples) with 4 ug/ml polybrene. Mock- infected MRC5 cells were treated with 4 ug/ml polybrene alone. 16-18 hours later, media was replaced with EMEM + 10% FBS and changed thereafter daily. Cells were harvested on day 5 by adding 1 ml Trizol to each well.
Growth protocol MRC5 (mock and infected) cells were maintained in Eagle's Minimal Essential Medium (EMEM, ATCC Cat # 30-2003) supplemented with 10% FBS
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with the Trizol reagent (1ml/ 6 well; ThermoFisher Cat # 15596-018) according to manufacturer's instructions
Label Cy3
Label protocol Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.
 
Hybridization protocol Following fragmentation, cRNA were hybridized for Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.
Scan protocol Slides were scanned using Illumina iScanner
Description MRC5 fibroblasts replicate 2
Male, MRC5 fibroblasts, five days following mock infection
Data processing The data were analyzed with GenomeStudio using Illumina default analysis settings
Quantile normalized and analyzed using Partek's Genomics Suite
 
Submission date May 25, 2016
Last update date Aug 30, 2017
Contact name Mark Ptashne
E-mail(s) m-ptashne@mskcc.org
Organization name Sloan Kettering Institute
Department Molecular Biology Program
Lab Mark Ptashne
Street address 1275 York Ave
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL10558
Series (2)
GSE81891 OCT4 and SOX2 Work as Transcriptional Activators in Reprogramming Human Fibroblasts
GSE81900 OCT4 and SOX2 Work as Transcriptional Activators in Reprogramming Human Fibroblasts

Data table header descriptions
ID_REF
VALUE Quantile normalized signal
Avg_NBEADS
BEAD_STDERR
Detection Pval

Data table
ID_REF VALUE Avg_NBEADS BEAD_STDERR Detection Pval
ILMN_1762337 2.457136 19 3.74371 0.3116883
ILMN_2055271 22.94998 14 10.2087 0.001298701
ILMN_1736007 15.73104 16 5.589618 0.01298701
ILMN_2383229 -5.461841 18 3.647053 0.8402597
ILMN_1806310 -0.08355157 15 2.523602 0.4896104
ILMN_1779670 -4.712136 21 2.86643 0.8103896
ILMN_1653355 22.22251 22 5.750895 0.001298701
ILMN_1717783 -8.279745 23 3.516774 0.9363636
ILMN_1705025 3.209545 20 3.34712 0.261039
ILMN_1814316 -1.479001 26 3.048003 0.5961039
ILMN_2359168 5.692156 17 4.134344 0.1415584
ILMN_1731507 -1.214137 27 3.48723 0.5727273
ILMN_1787689 7.026078 16 3.531925 0.09220779
ILMN_3241953 52.01762 24 7.204089 0
ILMN_1745607 205.2333 23 18.10503 0
ILMN_2136495 1.307227 25 3.393715 0.387013
ILMN_1668111 -6.929571 14 2.927474 0.8909091
ILMN_2295559 6.870056 17 3.162838 0.0987013
ILMN_1735045 53.63924 19 7.198263 0
ILMN_1680754 7.991977 20 5.098021 0.07402597

Total number of rows: 47322

Table truncated, full table size 1935 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap