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| Status |
Public on Feb 21, 2012 |
| Title |
H1_shRNA_DNMT3A_1_ctrl_p60_RRBS |
| Sample type |
SRA |
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| Source name |
hES H1 passage 60 infected with control shRNA against GFP
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hES_H1_p60
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| Growth protocol |
The pluripotent cell lines were grown in human ES media consisting of KO-DMEM (Invitrogen), 10% KOSR (Invitrogen), 10% plasmanate (Talecris), 1% glutamax or L-glutamin, nonessential amino acids, penicillin/streptomycin, 0.1% 2-mercaptoethanol and 10–20 ng/ml bFGF. All pluripotent cells were grown on a monolayer of irradiated CF1-MEFs (GlobalStem) and passaged using trypsin (0.05%) or dispase (Invitrogen). Before collection of DNA and RNA for analysis, ES and iPS cells were either isolated using trypsin (0.05%) or dispase, or plated on matrigel (BD Biosciences) for one passage and fed with human ES media conditioned in CF1-MEFs for 24 hr. The material from the rectal mucosa, rectal smooth muscle, skeletal muscle and stomach smooth muscle was obtained from MGH Pathology under the REMC project. human blood CD19 and CD34 samples were obtained from Shelly Heimfeld’s lab. Pancreatic islet samples were retrieved from the islet donor network and supplied by Stuart Schreibers Group.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
RRBS was performed according to a previously published protocol (Smith et al., 2009) with some optimizations for small cell numbers (Gu et al., 2010)
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
reduced representation bisulfite sequencing
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| Data processing |
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using MAQ bisulfite alignment mode.
References: Smith, Z. D., Gu, H., Bock, C., Gnirke, A. & Meissner, A. High-throughput bisulfite sequencing in mammalian genomes. Methods 48, 226-232, doi:S1046-2023(09)00111-X
Gu, H. et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7, 133-136, doi:nmeth.1414
Genome Build:
RRBS_cpgMethylation_H1_shRNA_DNMT3A_1_ctrl_p60.RRBS.bed: hg18
RRBS_cpaMethylation_H1_shRNA_DNMT3A_1_ctrl_p60.RRBS.bed: hg18
RRBS_cpcMethylation_H1_shRNA_DNMT3A_1_ctrl_p60.RRBS.bed: hg18
RRBS_cptMethylation_H1_shRNA_DNMT3A_1_ctrl_p60.RRBS.bed: hg18
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| Submission date |
Feb 20, 2012 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Michael Johannes Ziller |
| Organization name |
Max Planck Institute of Psychiatry
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| Department |
Translational Psychiatry
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| Lab |
Ziller lab
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| Street address |
Kraepelinstrasse 2-10
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| City |
Munich |
| ZIP/Postal code |
80804 |
| Country |
Germany |
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| Platform ID |
GPL9115 |
| Series (1) |
| GSE27432 |
Genomic distribution and inter-sample variation of non-CG methylation across human cell types |
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| Relations |
| BioSample |
SAMN02197589 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM877689_RRBS_cpaMethylation_H1_shRNA_DNMT3A_1_ctrl_p60.RRBS.bed.gz |
21.5 Mb |
(ftp)(http) |
BED |
| GSM877689_RRBS_cpcMethylation_H1_shRNA_DNMT3A_1_ctrl_p60.RRBS.bed.gz |
30.7 Mb |
(ftp)(http) |
BED |
| GSM877689_RRBS_cpgMethylation_H1_shRNA_DNMT3A_1_ctrl_p60.RRBS.bed.gz |
23.4 Mb |
(ftp)(http) |
BED |
| GSM877689_RRBS_cptMethylation_H1_shRNA_DNMT3A_1_ctrl_p60.RRBS.bed.gz |
25.5 Mb |
(ftp)(http) |
BED |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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