NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM603055 Query DataSets for GSM603055
Status Public on Mar 14, 2011
Title H9 ESC - replicate 2
Sample type RNA
 
Source name H9-ESC_2
Organism Homo sapiens
Characteristics cell line: h9-esc_2: H9 hESCs (WiCell Research)
Biomaterial provider WiCell Research
Growth protocol H9 hESCs (WiCell Research) and iPSCs were maintained on a layer of mitotically inactivated MEFs in DMEM/F12 (Invitrogen) supplemented with 0.1 mM non-essential amino acids (Invitrogen), 1 mM glutamax (Invitrogen), 20% Knockout Serum Replacement (Invitrogen), 55 μM b-mercaptoethanol (Invitrogen) and 10 ng/ml bFGF (Joint Protein Central). hESCs and iPSCs were also cultured in Matrigel (BD Biosciences) with mTeSR medium (Stem Cell Technologies).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol (Invitrogen) followed by cDNA synthesis using High capability RNA-to-cDNA Mater Mix (Invitrogen).
Label Biotin
Label protocol The GeneChip microarray processing was performed by the Functional Genomica Core in the Institute for Research in Biomedicine (Barcelona, Spain) according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). The amplification and labeling were processed as indicated in Nugen protocol with 25ng starting RNA. For each sample, 3.75ug ssDNA were labeled and hybridized to the Affymetrix HG-U133 Plus 2.0 chips.
 
Hybridization protocol The GeneChip microarray processing was performed by the Functional Genomica Core in the Institute for Research in Biomedicine (Barcelona, Spain) according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). The amplification and labeling were processed as indicated in Nugen protocol with 25ng starting RNA. For each sample, 3.75ug ssDNA were labeled and hybridized to the Affymetrix HG-U133 Plus 2.0 chips.
Scan protocol Expression signals were scanned on an Affymetrix GeneChip Scanner (7G upgrade). The data extraction was done by the Affymetrix GCOS software v.1.4.
Data processing The statistical analysis of the data was performed using ArrayStar 3. Briefly, raw CEL files were imported together with gene annotation from NetAffix (from 11/13/2009) and normalized using RMA algorithm and quantile normalization. As both H9 ESC and HGPS-iPSC originate from female samples, and in order to check for any possible bias introduced by the X and Y chromosome-coded genes, we performed the same analysis with only autosome genes.
 
Submission date Oct 01, 2010
Last update date Mar 14, 2011
Contact name Stephanie Boue
Organization name CMRB
Street address Dr Aiguader 88
City Barcelona
ZIP/Postal code 08003
Country Spain
 
Platform ID GPL570
Series (1)
GSE24487 Recapitulation of human premature aging by using iPSCs from Hutchinson-Gilford progeria syndrome

Data table header descriptions
ID_REF
VALUE RMA normalized autosome probes-only

Data table
ID_REF VALUE
222725_s_at 2.708913012
218736_s_at 3.240340318
232187_at 2.825680372
234359_at 7.116256617
234890_at 5.970535783
243252_at 6.614739703
1570207_at 2.557599365
223692_at 3.633229149
203566_s_at 10.48839906
242333_at 3.914808142
1569631_at 7.367223686
206770_s_at 8.939630413
209865_at 8.653291434
229852_at 5.99921664
226894_at 9.591568307
238881_at 6.66099981
225222_at 10.6115022
242374_at 7.103880925
230868_at 4.231855011
231895_at 8.882718172

Total number of rows: 51788

Table truncated, full table size 1147 Kbytes.




Supplementary file Size Download File type/resource
GSM603055.CEL.gz 5.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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