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| Status |
Public on Apr 12, 2023 |
| Title |
AML patient (UD5), methylation table, onset phase |
| Sample type |
SRA |
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| Source name |
bone marrow
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| Organism |
Homo sapiens |
| Characteristics |
phase: onset
disease state: AML
tissue: bone marrow
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cryopreserved bone marrow (BM) mononuclear cells using QIAGEN’s AllPrep DNA/RNA kit.
Genomic DNA by ligation SQK-LSK109 (Oxford Nanopore Technologies, ONT)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
GridION |
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| Description |
UD5_tum
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| Data processing |
DNA from each of three pairs of matched AMLs was sequenced on the GridION X5 instrument with a run-time of 48h by using five or six individual R9.4 flow
The reads generated by each run were base-called using Guppy v2.0.2
The reads generated by each run were base-called using Guppy v2.0.2
The and quality assessment was performed with NanoR and PyPore
High-quality pass reads were then aligned against the human reference genome (hg19) with minimap2
Assembly: hg19
Supplementary files format and content: Processed data files contain genomic coordinates (Chr, start, end), CpG found in the segment, methyalted CpG found in the segment
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| Submission date |
Sep 19, 2022 |
| Last update date |
Apr 12, 2023 |
| Contact name |
Gianluca Mattei |
| E-mail(s) |
gianluca.mattei@unifi.it
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| Organization name |
Università degli Studi di Firenze
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| Street address |
Via di S. Marta, 3
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| City |
Firenze |
| State/province |
FI |
| ZIP/Postal code |
50139 |
| Country |
Italy |
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| Platform ID |
GPL28975 |
| Series (2) |
| GSE213685 |
High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias. [methylation] |
| GSE213686 |
High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias. |
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| Relations |
| BioSample |
SAMN30818525 |
| SRA |
SRX17543022 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6592043_UD5_tum_methylation.tsv.gz |
169.4 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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