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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 19, 2017 |
| Title |
AML blast 2189 |
| Sample type |
SRA |
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| Source name |
AML blast cells
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| Organism |
Homo sapiens |
| Characteristics |
diagnosis: acute myeloid leukemia (AML)
cell type: blast
age: 53
gender: male
fab: M4E
cytogenetics: inv(16)
t(v;11q23): Neg
chr3q: Neg
chr5q: Neg
t(15;17): Neg
t(8;21): Neg
inv(16): Pos
tri(8): Neg
t(6;9): Neg
other: Neg
normal karyotype: Neg
flt3 itd: Neg
flt3 tkd: Neg
npm1: Neg
nras: Pos
kras: Neg
cebpa: Neg
kit: Pos
idh1: Neg
idh2: Neg
dnmt3a: Neg
dnmt3a amino acid mutation: --
evi1 overexpression: Neg
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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 HiSeq2000 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
Genome_build: hg19
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 |
Sep 15, 2016 |
| 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) |
| GSE86952 |
Epigenetic identity in AML is mostly dependent on disruption of non-promoter regulatory elements and reveals potentially antagonistic effects of mutations in epigenetic modifiers [human] |
| 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 |
SAMN05773243 |
| SRA |
SRX2164637 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2310825_methylcall.Sample_2189.mincov10.txt.gz |
33.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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