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Sample GSM603053 Query DataSets for GSM603053
Status Public on Mar 14, 2011
Title HGPS-iPSC replicate 2
Sample type RNA
 
Source name HGPS-iPSC_2
Organism Homo sapiens
Characteristics cell line: hgps-ipsc_2: Human HGPS fibroblasts AG01972, AG11498, AG06297, and normal fibroblasts GM00038 (9 year), AG05247 (87 year), AG09602 (92 year) were purchased from Coriell Cell Repository and reprogrammed using the protocol below.
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
Treatment protocol iPSCs Generation. For the generation of human iPSCs, human fibroblasts were seeded in a 6-well plate and spin-infected with a mix of high-quality retroviruses encoding OCT4, SOX2, KLF4, c-MYC, and GFP in the presence of 4 g/ml polybrene. Three infections on consecutive days were performed. 6 days after the first spin-infection, fibroblasts were gently individualized with TrypLE (invitrogen) and seeded onto fresh MEFs in the fibroblast culture medium. After 24 h, the medium was switched to hESC medium. The media was changed every 1–2 days depending on cell density. To establish the iPSC lines, colonies were manually picked and transferred onto MEF feeder cells for several passages before further transfer to Matrigel/mTesR conditions.
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 2.692152491
218736_s_at 3.184296743
232187_at 2.676784049
234359_at 7.163858743
234890_at 5.617713044
243252_at 6.712044848
1570207_at 2.530864339
223692_at 3.723325381
203566_s_at 10.39025043
242333_at 3.467916339
1569631_at 6.889974811
206770_s_at 8.922940911
209865_at 8.363646418
229852_at 5.47885814
226894_at 9.578673323
238881_at 6.084694456
225222_at 10.51618767
242374_at 6.965359503
230868_at 4.137392913
231895_at 8.752462867

Total number of rows: 51788

Table truncated, full table size 1147 Kbytes.




Supplementary file Size Download File type/resource
GSM603053.CEL.gz 5.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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