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| Status |
Public on Sep 15, 2011 |
| Title |
human_hspc |
| Sample type |
SRA |
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| Source name |
HSPC
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| Organism |
Homo sapiens |
| Characteristics |
developmental stage: progenitor
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Bisulfite sequencing libraries were generated by previously described methods (Hodges et al., 2009) and on the manufacturer's instructions (Illumina) but with several additional modifications. Briefly, following each enzymatic step, genomic DNA was recovered by phenol:chloroform extraction and ethanol precipitation. Adenylated fragments were ligated to Illumina-compatible paired-end adaptors synthesized with 5'-methyl-cytosine and, when necessary, adaptors were diluted 100-1000x to compensate for low-input libraries and maintain an approximate 10-fold excess of adaptor oligonucleotides. Following ligation, DNA fragments were purified and concentrated on MinElute columns (Qiagen). The standard gel purification step for size selection was excluded from the protocol. Fragments were denatured and treated with sodium bisulfite using the EZ DNA Methylation Gold kit according to the manufacturer's instructions (Zymo). Lastly, the sample was desulfonated and the converted, adaptor-ligated fragments were PCR enriched using paired-end adaptor-compatible primers 1.0 and 2.0 (Illumina) and the Expand High Fidelity Plus PCR system (Roche). Paired-end Illumina sequencing was performed on bisulfite converted libraries for 76-100 cycles each end. Average insert length were 150-200bp.
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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 |
Bisulfite converted
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| Data processing |
Each Sample contains processed data file corresponding to the hypomethylated_regions, cpg_methylation_levels, and cpg_read_coverages
Alignment: Mapping bisulfite treated reads was done with methods described by Smith et al. (2009) using tools from the RMAP package (Smith et al., 2009).
HMR detection: Hypomethylated regions (HMRs) were identified using a hidden Markov model as described in Molaro et al. (Cell 146, 1-13, September 16, 2011).
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| Submission date |
Sep 07, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew D Smith |
| E-mail(s) |
andrewds@usc.edu
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| Organization name |
University of Southern California
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| Department |
Molecular and Computational Biology
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| Lab |
Smith Lab
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| Street address |
1050 Childs Way
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
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| Platform ID |
GPL9115 |
| Series (1) |
| GSE31971 |
Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment |
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| Relations |
| Reanalyzed by |
GSE46644 |
| SRA |
SRX096518 |
| SRA |
SRX096521 |
| BioSample |
SAMN00716608 |
| Named Annotation |
GSM791828_human_hspc_hmr_hg18.bed.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM791828_human_hspc_CpG_coverage_hg18.bedgraph.gz |
174.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM791828_human_hspc_CpG_methylation_hg18.bedgraph.gz |
188.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM791828_human_hspc_hmr_hg18.bed.gz |
833.6 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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