|
| Status |
Public on Nov 17, 2014 |
| Title |
ICF1-1 iPS (MethylC-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
induced pluripotent stem cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: induced pluripotent stem cell
|
| Treatment protocol |
hiPSCs were maintained in DME supplemented with 20% KSR, nonessential amino acids (Invitrogen), L-Glutamine (Mediatech), Penn/Strep, 2-mercaptoethanol with a feeder layer of MEFs as previously described (Shen et al., 2006).
|
| Growth protocol |
ICF hiPSCs were generated by using transducing ICF patient fibroblasts with Yamanaka factors
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
hiPSCs were passaged onto feeder free gelatin coated plates twice before harvesting DNA
Library construction was performed following Illumina manufacturer suggestions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
bisulfite converted genomic DNA
|
| Data processing |
Each sample was subjected to sequencing according to manufacturer’s instruction with Illumina Hiseq 2000.
Reads were mapped to the hg18 genome via BS-Seeker
BED files contain the ratio of methylated cytosines to total cytosines covered at single base position
only cytosines with at least 3 or more covered reads were considered
Genome_build: hg18
Supplementary_files_format_and_content: ICF1-1iPS_CG.bed BED file of all CG methylation covered by at least 3 reads
Supplementary_files_format_and_content: ICF1-2iPS_CG.bed BED file of all CG methylation covered by at least 3 reads
|
| |
|
| Submission date |
Jun 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Huang |
| Phone |
310-267-0438
|
| Organization name |
UCLA
|
| Department |
Human Genetics
|
| Lab |
Guoping Fan
|
| Street address |
Gonda BLDG Rm. 6554, P.O.Box 957088
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7088 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE46030 |
Selective demethylation and altered gene expression are associated with ICF Syndrome in human induced pluripotent stem cells and mesenchymal stem cells |
|
| Relations |
| BioSample |
SAMN02842722 |
| SRA |
SRX576045 |
