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| Status |
Public on May 28, 2014 |
| Title |
H9 RPE |
| Sample type |
SRA |
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| Source name |
retinal pigmented epithelium
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| Organism |
Homo sapiens |
| Characteristics |
cell type: ES-derived RPE
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| Treatment protocol |
Cells were cultured at 37℃ in 5% CO2 for 6-10 days after which zfbFGF was omitted to facilitate spontaneous cell differentiation.
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| Growth protocol |
Pluripotent stem cells (hESC and iPSCs) were plated onto gamma-rays irradiation mouse embryonic feeder cells with DMEM/F12 culture medium containing 20% Knock-Out Serum Replacement, 0.1 mM nonessential amino acids, 0.1 mM b-mercaptoethanol and 100 ng/ml zebrafish basic fibroblast growth factor (zfbFGF) on a 6-well plate. RPE medium were changed to support pigment cluster expansion [containing α-MEM, 1×N2 supplement(Gibco), 1×Non-essential amino acid solution, 250 mg/ml taurine, 13 ng/ml Triiodo thyronin (Sigma-Aldrich, Gillingham, UK), 20 ng/ml Hydrocortisone (Sigma), 2 mM L-glutamine (Invitrogen, Paisley, UK), 1×Penicillin-streptomycin and 10% Hyclone heat-inactivat-ed foetal bovine serum (Thermo Scientific, Northumberland, UK)], which was replaced daily.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from all samples by traditional phenol/chloroform method.
One µg genomic DNA was digested with the methylation insensitive restriction enzyme MspI (NEB). Ends of each restriction fragment were filled in and a 3′ adenosine was added with Klenow Fragment (3′→5′ exo-minus; NEB). Methylated paired-end Illumina adapters were ligated to the ends of the DNA fragments using T4 DNA Ligase (NEB). Fragments between 100 bp and 400 bp were purified by agarose gel extraction. The purified fragments were treated with sodium bisulfite and then amplified by PCR.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 6
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| Data processing |
Each sample was subjected to sequencing according to manufacturer’s instruction with Illumina Hiseq 2000.
Reads were prefiltered by trimming away adapter sequences and selecting reads that contain 5' MspI site
Reads were mapped to the hg18 genome via BS-Seeker
wiggle files contain the ratio of methylated cytosines to total cytosines covered at single base position
only cytosines with at least 5 or more covered reads were considered
Genome_build: hg18
Supplementary_files_format_and_content: wiggle files containing the ratio of methylated cytosines to total cytosines covered at single base position
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| Submission date |
Jan 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Huang |
| Phone |
310-267-0438
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| Organization name |
UCLA
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| Department |
Human Genetics
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| Lab |
Guoping Fan
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| Street address |
Gonda BLDG Rm. 6554, P.O.Box 957088
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7088 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE43473 |
Integrated analysis of DNA methylation and RNA transcriptome during the differentiation of human pluripotent stem cells into retinal pigment epithelial cells |
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| Relations |
| SRA |
SRX216800 |
| BioSample |
SAMN01886268 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1063310_H9RPE2.wig.gz |
4.5 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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