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Sample GSM603015 Query DataSets for GSM603015
Status Public on Mar 14, 2011
Title BJ-fib_1
Sample type RNA
 
Source name BJ fibroblasts
Organism Homo sapiens
Characteristics cell line: bj-fib_1: BJ (CRL-2522) fibroblasts were purchased from ATCC.
Biomaterial provider ATCC
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 2.607681586
218736_s_at 3.240340318
232187_at 2.953302472
234359_at 6.389588932
234890_at 5.913746123
243252_at 7.750369194
1570207_at 2.298536431
223692_at 6.076843271
203566_s_at 10.03671083
242333_at 3.65305348
1569631_at 9.318772034
206770_s_at 10.15426336
209865_at 9.367022999
229852_at 7.489076397
226894_at 10.18509923
238881_at 7.212613869
225222_at 11.29911295
242374_at 8.034075908
230868_at 6.052266886
231895_at 7.951493258

Total number of rows: 51788

Table truncated, full table size 1147 Kbytes.




Supplementary file Size Download File type/resource
GSM603015.CEL.gz 5.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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