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Sample GSM1614006 Query DataSets for GSM1614006
Status Public on Apr 15, 2015
Title iPSC PiZZ T24 3
Sample type genomic
Source name PiZZ skin fibroblasts
Organism Homo sapiens
Characteristics cell line: iPSC
Stage: T24
group: iPSC PiZZ
Treatment protocol Aside from differentiation and sorting as described above, cells were not treated in any specific manner prior to DNA/RNA extraction.
Growth protocol iPSC and ESC lines were maintained in “hiPSC Media” composed of DMEM/F12 (Sigma-Aldrich, with 20% KnockOut Serum Replacement (Invitrogen,, 1mM nonanimal L-glutamine (Sigma-Aldrich), 0.1mM Β-mercaptoethanol, and 10 ng/ml FGF2 (R&D Systems, Minneapolis, MN) on 0.1% gelatin (Sigma-Aldrich) coated plates preseeded with mitomycin C-inactivated or irradiated mouse embryonic fibroblast (MEF) feeder cells. Cells were maintained in a 5% CO2 air environment. For endodermal differentiation, cells were passed onto matrigel-coated dishes at 80% confluency. On the following day, designated “T0”, differentiation was induced by culture in media containing growth factors listed below. From T0-T6, differentiation media included 2mM l-glutamine, and 4.5x10-4 M monothioglycerol (MTG). Cells were grown in T0 media, consisting of RPMI-based serum-free medium with Chir 99021 (2ug/ml) and Activin A (100 ng/ml), for one day. On days “T1-2”, medium was changed to RPMI with BMP4 (0.5 ng/ml), FGF2 (10ng/ml), Activin A (100 ng/ml), and VEGF (10 ng/ml). On days “T3-4”, cells were cultured in SFD media(Gouon-Evans et al., 2006) with BMP4 (0.5 ng/ml), FGF2 (10ng/ml), Activin A (100 ng/ml), and VEGF (10 ng/ml). For hepatic differentiation, PSCs were differentiated as monolayer cultures as outlined above to generate definitive endoderm and then further differentiated for an additional 3 weeks in SFD-based media with ascorbic acid (50mcg/ml), monothioglycerol (4.5x10-4 M ), and the following supplements: T7-12: BMP4 (50 ng/ml), FGF2 (10 ng/ml), VEGF (10 ng/ml), EGF (10ng/ml), TGFa (20 ng/ml), HGF (100 ng/ml), and 0.1 uM Dexamethasone; T13-18: FGF2 (10 ng/ml), VEGF (10 ng/ml), EGF (10 ng/ml), HGF (100 ng/ml), Oncostatin M (20 ng/ml), Vitamin K (6 ug/ml), 1.5 uM gamma secretase inhibitor, 0.1 uM Dexamethasone, and 1% DMSO; T19-24: HGF (100 ng/ml), Oncostatin M (20 ng/ml), Vitamin K (6 ug/ml), and 0.1 uM Dexamethasone. Differentiating human PSCs were maintained in a 5% CO2, 5% O2, 90% N2 environment.
Extracted molecule genomic DNA
Extraction protocol According to Illumina protocol
Label Cy5 and Cy3
Label protocol 500ng gDNA underwent bisulfite conversion of unmethylated cytosine bases to uracil, and bisulfite converted DNA was then amplified and purified
Hybridization protocol Overnight hybridization to BeadChip arrays.
Scan protocol Next day staining of hybridized arrays produced methylation-dependent differential fluorescence that was detected via an Illumina iScan array scanner.
Description Sample name: 103 T24
Gene methylation data from PiZZ skin fibroblasts profiled at T24.
Data processing Arrays were visualized and processed using the GenomeStudio software package, which produced IDAT files that were read into a MethyLumiSet using the methylumIDAT function in the methylumi R package (version 2.4.0). This object was then coerced to a MethyLumiM object and quantile-normalized by sequentially applying the lumiMethyC and lumiMethyN functions from the lumi R package (version 2.10.0). All methylation analyses were performed using the R environment for statistical computing (version 2.15.1).
Submission date Feb 19, 2015
Last update date Apr 16, 2015
Contact name Adam C Gower
Phone 617-358-7138
Organization name Boston University School of Medicine
Department Department of Medicine
Lab Division of Computational Biomedicine
Street address 72 East Concord Street, E632
City Boston
State/province MA
ZIP/Postal code 02118
Country USA
Platform ID GPL13534
Series (2)
GSE66077 Emergence of a developmental stage-dependent human liver disease signature demonstrated by directed differentiation of alpha-1 antitrypsin deficient iPS cells [HumanMethylation450]
GSE66078 Emergence of a developmental stage-dependent human liver disease signature demonstrated by directed differentiation of alpha-1 antitrypsin deficient iPS cells

Data table header descriptions
VALUE M values

Data table
cg00000029 0.758707055 0
cg00000108 3.391919766 0
cg00000109 3.012764195 0
cg00000165 -2.062478124 0
cg00000236 2.73312522 0
cg00000289 1.296434717 0
cg00000292 2.960557525 0
cg00000321 -2.078874976 0
cg00000363 -2.438726518 0
cg00000622 -4.033418121 0
cg00000658 1.883650397 0
cg00000714 -2.397593079 0
cg00000721 2.447680327 0
cg00000734 -2.741278917 0
cg00000769 -2.701281954 0
cg00000807 2.400329873 0
cg00000884 1.642803969 0
cg00000905 -2.48931897 0
cg00000924 0.285016547 0
cg00000948 2.564229397 0

Total number of rows: 485577

Table truncated, full table size 12030 Kbytes.

Supplementary file Size Download File type/resource
GSM1614006_8221916159_R03C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1614006_8221916159_R03C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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