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| Status |
Public on Nov 23, 2022 |
| Title |
AML, DR79 |
| Sample type |
SRA |
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| Source name |
AML
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| Organism |
Homo sapiens |
| Characteristics |
disease state: AML
aml status: tAML
fab: M4
cell type: leukemia blast cells
sample type: AML diagnosis sample
age: 40
Sex: f
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracte with mirRNeay mini kit (NEB).
100 ng total RNA was fragmented by alkaline hydrolysis at 95°C for 12 min. to achieve a fragment length of about 30 nucleotides. Libraries were prepared using the NEBNext® Small RNA library prep kit.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
DR79
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| Data processing |
Library strategy: Ribometh-Seq
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina NextSeq500
Adapter sequences were removed using Cutadapt with a minimum length of 15 nt,
Reads were mapped using Bowtie2 to a reference sequence file containing rDNA sequences of U18, U28 and U5.8S
For each position the number of 5’-read ends was counted.
2’O-methyation was calculated as scoreC based on 5’-end frequencies as described before by Birkedal et al., 2015
Genome_build: Annotation of modification sites as well as rRNA sequence was downloaded from https://www-snorna.biotoul.fr. Furthermore we considered novel sites reported by Krogh 2016, Jorjani 2016 and Sharma 2017.
Supplementary_files_format_and_content: RiboMethSeq_scoreC.txt contains calculated scoreC for annotated modification sites: subunit TAB pos TAB annotation TAB sample_scoreC
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| Submission date |
Sep 24, 2021 |
| Last update date |
Nov 23, 2022 |
| Contact name |
Christian Rohde |
| E-mail(s) |
[email protected]
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| Organization name |
Heidelberg University
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| Lab |
Molecular Hematology and Oncology
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| Street address |
Im Neuenheimer Feld 410
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| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE184727 |
The dynamic rRNA ribomethylome drives stemness in acute myeloid leukemia [ribomethseq_primary_samples] |
| GSE184728 |
The dynamic rRNA ribomethylome drives stemness in acute myeloid leukemia |
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| Relations |
| BioSample |
SAMN21593694 |
| SRA |
SRX12326669 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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