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| Status |
Public on Mar 02, 2020 |
| Title |
L-MPP-1 |
| Sample type |
SRA |
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| Source name |
L-MPP
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| Organism |
Homo sapiens |
| Characteristics |
tissue type: primary
cell type: L-MPP
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Epicentre DNA extraction kit
Whole Genome Bisulfite Sequencing; Illumina TruSeq, NEBNext
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
base calls and demultiplexing: bcl2fastq v1.8.4
Trim Galore! v0.3.6
Bismark v0.12.3
InformME
Genome_build: hg19
Supplementary_files_format_and_content: bed format. Tracks include mean methylation level (MML), normalized methylation entropy (NME), methylation sensitivity index (MSI), and differential quantities of the above between samples (dMML, dNME, dMSI) and Jensen Shannon Distance (JSD) to measure epigenetic discordance between samples, as well as tracks of differentially methylated regions (DMR) based on JSD.
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| Submission date |
Aug 15, 2019 |
| Last update date |
Jan 07, 2022 |
| Contact name |
Michael A Koldobskiy |
| Organization name |
Johns Hopkins University
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| Department |
Center for Epigenetics
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| Lab |
Rangos 573
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| Street address |
855 N. Wolfe St.
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE135869 |
DNA Methylation Potential Energy Landscape Analysis of MLL-rearranged Acute Myeloid Leukemia (AML) and Normal hematopoietic precursors [WGBS] |
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| Relations |
| BioSample |
SAMN12583133 |
| SRA |
SRX13625881 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4036933_MML-Normal-L-MPP-1.bed.gz |
86.4 Mb |
(ftp)(http) |
BED |
| GSM4036933_MSI-Normal-L-MPP-1.bed.gz |
87.7 Mb |
(ftp)(http) |
BED |
| GSM4036933_NME-Normal-L-MPP-1.bed.gz |
88.9 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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