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Sample GSM603044 Query DataSets for GSM603044
Status Public on Mar 14, 2011
Title HGPS Fibroblast replicate 1
Sample type RNA
 
Source name HGPS-fib_1
Organism Homo sapiens
Characteristics cell line: hgps-fib_1: Human HGPS fibroblasts AG01972, AG11498, AG06297, and normal fibroblasts GM00038 (9 year), AG05247 (87 year), AG09602 (92 year) were purchased from Coriell Cell Repository
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=AG01972
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=AG11498
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=AG06297
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM00038
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=AG05247
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=AG09602
Growth protocol All fibroblasts were cultured in 5% CO2 and at 37°C in DMEM containing 15% FBS, 2 mM L-glutamine, 0.1 mM non-essential aminoacids, sodium Pyruvate, and 55 μM b-mercaptoethanol.
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 3.821062876
218736_s_at 7.106301949
232187_at 3.110569175
234359_at 6.667840213
234890_at 5.931904896
243252_at 7.561962229
1570207_at 2.414812589
223692_at 6.285579924
203566_s_at 11.25801726
242333_at 3.771325026
1569631_at 9.640375815
206770_s_at 11.24610492
209865_at 10.03510965
229852_at 8.110025525
226894_at 11.39447587
238881_at 7.734902703
225222_at 12.08255643
242374_at 7.865780652
230868_at 5.516750389
231895_at 9.084142202

Total number of rows: 51788

Table truncated, full table size 1147 Kbytes.




Supplementary file Size Download File type/resource
GSM603044.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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