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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 28, 2017 |
| Title |
BMT696_2143 |
| Sample type |
SRA |
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| Source name |
AML blast cells
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| Organism |
Homo sapiens |
| Characteristics |
genotype/variation: WT LSK
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| Treatment protocol |
The hematopoietic stem cells, characterized by lin-, Sca+, and cKit+, were sorted from mice.
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| Growth protocol |
Primary, uncultured cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Enhanced reduced representation of bisulfite sequencing (PMC4354670): High molecular weight genomic DNA was digested with MspI restriction enzyme, subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina adaptors. Fragments of 150-400 bp were isolated by size selection and subjected to bisulfite conversion and PCR amplification using paired-end Illumina primers. Libraries were sequenced using an Illumina HiSeq2500 per manufacturer’s recommended protocol for 50bp single end read reads
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Casava 1.7 for base calling
Adapter trimming with FAR 2.15
Alignment with Bowtie 0.12.7
Methylation calling with Bismark 0.5.4
Idh2 R140Q alignments were made to mm9, then transferred to mm10 using liftOver. Idh2 R140Q / Dnmt3a R878H alignments were made directly to mm10.
Genome_build: mm10
Supplementary_files_format_and_content: Files are in text format with the following 7 columns: chrBase, chr, base, strand, coverage, freqC, freqT. 'chrBase' is a concatenation of chromosome and base position for easy indexing. 'chr' is the chromosome, 'base' is the base position, 'coverage' ranges from 10-400. 'freqC' is the 'C' frequency representing the % of methylated bases and 'freqT' is the 'T' frequency, representing unmethylated bases.
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| Submission date |
Mar 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jacob Lowell Glass |
| Organization name |
Memorial Sloan Kettering Cancer Center
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| Street address |
1275 York Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE96744 |
Epigenetic identity in AML is mostly dependent on disruption of non-promoter regulatory elements and reveals potentially antagonistic effects of mutations in epigenetic modifiers [mouse] |
| GSE98350 |
Epigenetic identity in AML is mostly dependent on disruption of non-promoter regulatory elements and reveals potentially antagonistic effects of mutations in epigenetic modifiers |
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| Relations |
| BioSample |
SAMN06847841 |
| SRA |
SRX2769086 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2539363_methylcall.CpG.BMT696_2143.mincov0.txt.gz |
15.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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