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Sample GSM1089648 Query DataSets for GSM1089648
Status Public on Aug 16, 2013
Title iPS cells rep2
Sample type RNA
 
Source name Induced pluripotent stem cells derived from adult fibroblasts (day 0)
Organism Homo sapiens
Characteristics age: day 0
tissue: cultured cells
genotype: wild-type
cell type: induced pluripotent stem cells derived from adult fibroblasts
Treatment protocol not applicable
Growth protocol Human integration-free iPS cells cells were maintained on growth factor reduced matrigel (BD) in mTesR1 medium (STEMcell Techonologies). Cells were passaged every 3-4 days with accutase (Millipore) and replated with mTesR1 supplemented with 10µM Y-27632 (Millipore), with media daily media change. To initiate differentiation, cells were plated at a density of 1.04x104 cells/cm2 on growth factor reduced matrigel in N2B27-CDM (DMEM/F12 medium containing 1% N2 supplement, 2% B27 supplement, 0.05% BSA fraction V, 1% Glutamax, 1% MEM-NEAA, and 110µM 2-mercaptoethanol (Life Technologies), supplemented with 10µM Y-27632 and 20ng/mL ß-FGF (Peptrotech). Twenty-four hours later, N2B27-CDM was replaced without Y-27632. Once cells reach approximately 60% confluency, cells were treated with mixture of KSR:N2 media (KSR: KO DMEM medium containing 15% knockout serum replacement, 1% glutamax, 1% MEM-NEAA, 55µM 2-mercaptoethanol; N2: DMEM/F12 medium containing 0.15% glucose, 1% N2 supplement, 20µg/mL insulin, 5mM HEPES) (Life Technologies) supplemented with 50nM LDN-13189 (Stemgent) and 5µM SB431542 (Tocris) on day 1 (100:0), day 2 (75:25), day 3 (50:50), day 4 (25:75), and day 5 (0:100). Twenty-four hours later, NC cells were harvested with accutase or TryplE (Invitrogen) and prepared for analyses or maintenance on growth factor reduced matrigel in SFM media (KO DMEM/F12 medium containing 2% StemPro Neural supplement and 1% glutamax) (Life Technologies) supplemented with 20ng/mL ß-FGF and 20ng/mL EGF (Sigma). To passage NC cells, cells were rinsed once with PBS and treated with accutase for 3 minutes. Cells were collected, pelleted, and re-plated at a density of 3x104 cells/cm2 on growth factor reduced matrigel (BD), fibronectin (Roche) or CellStart (Invitrogen) and grown in either N2 or SFM. When cells were 80-90% confluent, they were passaged.
Extracted molecule total RNA
Extraction protocol Total RNA from biological triplicates of healthy donor fibroblast reprogrammed iPS cells and differentiated NC iPS cells were extracted with Trizol and prepared for hybridization to Human Gene 1.0 ST Affymetrix microarrays using ~1 µg of starting material.
Label biotin
Label protocol According to manufacturer's (Affymetrix) recommendations
 
Hybridization protocol According to manufacturer's (Affymetrix) recommendations
Scan protocol According to manufacturer's (Affymetrix) recommendations
Description Integration-free IPS cells were derived from a single healthy donor fibroblast. Replicates were obtained from independent cell culture wells.
Data processing Data were analyzed in AltAnalyze version 2.0.8 (http://altanalyze.org) using RMA (bundled Affymetrix Power Tools). Ensembl gene-level estimates were derived using the mean expression of all AltAnalyze constitutive annotated probesets (database: EnsMart65).
probe group file: HuGene-1_0-st-v1.r4.pgf
 
Submission date Feb 27, 2013
Last update date Aug 17, 2013
Contact name Nathan Salomonis
E-mail(s) nathan.salomonis@cchmc.org
Organization name Cincinnati Children's Hospital
Department Biomedical Informatics
Lab Nathan Salomonis
Street address 3333 Burnet Avenue
City Cincinnati
State/province OH
ZIP/Postal code 45229
Country USA
 
Platform ID GPL10739
Series (1)
GSE44727 A Robust Method To Derive Functional Neural Crest Cells From Human Pluripotent Stem Cells

Data table header descriptions
ID_REF
VALUE RMA probeset-level expression values

Data table
ID_REF VALUE
7892501 2.60086
7892502 3.89151
7892503 3.50148
7892504 8.09845
7892505 2.3935
7892506 3.83729
7892507 4.05735
7892508 4.10845
7892509 11.21851
7892510 2.0437
7892511 3.20806
7892512 6.39436
7892513 2.37942
7892514 8.78891
7892515 9.38309
7892516 6.95382
7892517 4.7118
7892518 1.89035
7892519 3.58475
7892520 8.51414

Total number of rows: 257430

Table truncated, full table size 3999 Kbytes.




Supplementary file Size Download File type/resource
GSM1089648_05.iPS_2.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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