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| Status |
Public on Nov 23, 2022 |
| Title |
The dynamic rRNA ribomethylome drives stemness in acute myeloid leukemia [ribomethseq_primary_samples] |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Eukaryotic ribosomal RNA carries diverse posttranscriptional modifications, the function of which are mostly unexplored. The evolutionarily conserved 2’-O-methylation (2’-O-Me) occurs at more than 100 sites and is essential for ribosome biogenesis. Plasticity of 2´-O-Me in ribosomes and its functional consequences in human disease remain to be elucidated. We performed RiboMethSeq to estabolish the full rRNA 2’-O-Me landscape (ribomethylome) in human acute myeloid leukemia (AML) through profiling 94 patient samples as well as 21 normal hematopoietic samples of 5 different lineages. The gene expression in the same samples was determined by RNA-Seq. We found that higher 2’-O-methylation on exterior dynamic sites associated with leukemia stem cell (LSC) signatures.
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| Overall design |
94 primary AMLs and 21 normal hematopoeitic cells of 5 different lineages was used for RiboMethSeq. The gene expression profiling in the same samples was determined by RNA-Seq. The association of rRNA 2’-O-Me pattern was confirmed with second independent AML cohort.
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| Contributor(s) |
Rohde C, Zhou F, Müller-Tidow C |
| Citation(s) |
36259929 |
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| Submission date |
Sep 24, 2021 |
| Last update date |
Nov 24, 2022 |
| Contact name |
Christian Rohde |
| E-mail(s) |
christian.rohde@uni-heidelberg.de
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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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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (148)
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| GSM5596427 |
AML, 04H112 |
| GSM5596428 |
AML, 05H050 |
| GSM5596429 |
AML, 05H094 |
| GSM5596430 |
AML, 05H181 |
| GSM5596431 |
AML, 06H028 |
| GSM5596432 |
AML, 06H135 |
| GSM5596433 |
AML, 09H043 |
| GSM5596434 |
AML, 09H115 |
| GSM5596435 |
AML, 10H056 |
| GSM5596436 |
AML, 10H101 |
| GSM5596437 |
AML, 11H006 |
| GSM5596438 |
AML, 11H009 |
| GSM5596439 |
AML, 11H095 |
| GSM5596440 |
AML, 11H129 |
| GSM5596441 |
AML, 11H142 |
| GSM5596442 |
AML_subpopulation, 119CD34negativeCD38positive |
| GSM5596443 |
AML_subpopulation, 119CD34positiveCD38negative |
| GSM5596444 |
AML_subpopulation, 119CD34positiveCD38positive |
| GSM5596445 |
AML_subpopulation, 145CD34negativeCD38positive |
| GSM5596446 |
AML_subpopulation, 145CD34positiveCD38negative |
| GSM5596447 |
AML_subpopulation, 145CD34positiveCD38positive |
| GSM5596448 |
B Cell, CD191 |
| GSM5596449 |
B Cell, CD193 |
| GSM5596450 |
B Cell, CD195 |
| GSM5596451 |
T cell, CD31 |
| GSM5596452 |
T cell, CD32 |
| GSM5596453 |
T cell, CD33 |
| GSM5596454 |
HSPC, CD34s1 |
| GSM5596455 |
HSPC, CD34s10 |
| GSM5596456 |
HSPC, CD34s11 |
| GSM5596457 |
HSPC, CD34s12 |
| GSM5596458 |
HSPC, CD34s2 |
| GSM5596459 |
T cell, CD35 |
| GSM5596460 |
AML, DR01 |
| GSM5596461 |
AML, DR02 |
| GSM5596462 |
AML, DR03 |
| GSM5596463 |
AML, DR04 |
| GSM5596464 |
AML, DR05 |
| GSM5596465 |
AML, DR06 |
| GSM5596466 |
AML, DR07 |
| GSM5596467 |
AML, DR08 |
| GSM5596468 |
AML, DR09 |
| GSM5596469 |
AML, DR10 |
| GSM5596470 |
AML, DR11 |
| GSM5596471 |
AML, DR12 |
| GSM5596472 |
AML, DR13 |
| GSM5596473 |
AML, DR14 |
| GSM5596474 |
AML, DR15 |
| GSM5596475 |
AML, DR16 |
| GSM5596476 |
AML, DR17 |
| GSM5596477 |
AML, DR18 |
| GSM5596478 |
AML, DR19 |
| GSM5596479 |
AML, DR20 |
| GSM5596480 |
AML, DR21 |
| GSM5596481 |
AML, DR22 |
| GSM5596482 |
AML, DR23 |
| GSM5596483 |
AML, DR25 |
| GSM5596484 |
AML, DR26 |
| GSM5596485 |
AML, DR27 |
| GSM5596486 |
AML, DR28 |
| GSM5596487 |
AML, DR29 |
| GSM5596488 |
AML, DR30 |
| GSM5596489 |
AML, DR31 |
| GSM5596490 |
AML, DR32 |
| GSM5596491 |
AML, DR33 |
| GSM5596492 |
AML, DR34 |
| GSM5596493 |
AML, DR36 |
| GSM5596494 |
AML, DR38 |
| GSM5596495 |
AML, DR39 |
| GSM5596496 |
AML, DR40 |
| GSM5596497 |
AML, DR41 |
| GSM5596498 |
AML, DR42 |
| GSM5596499 |
AML, DR43 |
| GSM5596500 |
AML, DR44 |
| GSM5596501 |
AML, DR46 |
| GSM5596502 |
AML, DR47 |
| GSM5596503 |
AML, DR48 |
| GSM5596504 |
AML, DR49 |
| GSM5596505 |
AML, DR50 |
| GSM5596506 |
AML, DR51 |
| GSM5596507 |
AML, DR52 |
| GSM5596508 |
AML, DR53 |
| GSM5596509 |
AML, DR54 |
| GSM5596510 |
AML, DR55 |
| GSM5596511 |
AML, DR56 |
| GSM5596512 |
AML, DR57 |
| GSM5596513 |
AML, DR58 |
| GSM5596514 |
AML, DR59 |
| GSM5596515 |
AML, DR60 |
| GSM5596516 |
AML, DR61 |
| GSM5596517 |
AML, DR62 |
| GSM5596518 |
AML, DR64 |
| GSM5596519 |
AML, DR65 |
| GSM5596520 |
AML, DR66 |
| GSM5596521 |
AML, DR67 |
| GSM5596522 |
AML, DR68 |
| GSM5596523 |
AML, DR69 |
| GSM5596524 |
AML, DR70 |
| GSM5596525 |
AML, DR71 |
| GSM5596526 |
AML, DR72 |
| GSM5596527 |
AML, DR73 |
| GSM5596528 |
AML, DR74 |
| GSM5596529 |
AML, DR75 |
| GSM5596530 |
AML, DR76 |
| GSM5596531 |
AML, DR77 |
| GSM5596532 |
AML, DR78 |
| GSM5596533 |
AML, DR79 |
| GSM5596534 |
AML, DR80 |
| GSM5596535 |
AML, DR81 |
| GSM5596536 |
AML, DR82 |
| GSM5596537 |
AML, DR83 |
| GSM5596538 |
AML, DR84 |
| GSM5596539 |
AML, DR85 |
| GSM5596540 |
AML, DR86 |
| GSM5596541 |
AML, DR87 |
| GSM5596542 |
AML, DR88 |
| GSM5596543 |
AML, DR89 |
| GSM5596544 |
AML, DR90 |
| GSM5596545 |
AML, DR91 |
| GSM5596546 |
AML, DR92 |
| GSM5596547 |
AML, DR93 |
| GSM5596548 |
AML, DR94 |
| GSM5596549 |
AML, DR95 |
| GSM5596550 |
AML, DR96 |
| GSM5596551 |
AML, DR97 |
| GSM5596552 |
AML, DR98 |
| GSM5596553 |
AML, DR99 |
| GSM5596554 |
Granulocyte, Granulocyte2 |
| GSM5596555 |
Granulocyte, Granulocyte3 |
| GSM5596556 |
Granulocyte, Granulocyte4 |
| GSM5596557 |
Granulocyte, Granulocyte5 |
| GSM5596558 |
AML_subpopulation, HD57CD34negCD38pos |
| GSM5596559 |
AML_subpopulation, HD57CD34posCD38neg |
| GSM5596560 |
AML_subpopulation, HD57CD34posCD38pos |
| GSM5596561 |
AML_subpopulation, HD72CD34negCD38pos |
| GSM5596562 |
AML_subpopulation, HD72CD34posCD38neg |
| GSM5596563 |
AML_subpopulation, HD72CD34posCD38pos |
| GSM5596564 |
AML_subpopulation, HD77CD34negCD38pos |
| GSM5596565 |
AML_subpopulation, HD77CD34posCD38neg |
| GSM5596566 |
AML_subpopulation, HD77CD34posCD38pos |
| GSM5596567 |
Monocyte, Monocyte1 |
| GSM5596568 |
Monocyte, Monocyte2 |
| GSM5596569 |
Monocyte, Monocyte3 |
| GSM5596570 |
Monocyte, Monocyte4 |
| GSM5596571 |
Monocyte, Monocyte5 |
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| This SubSeries is part of SuperSeries: |
| GSE184728 |
The dynamic rRNA ribomethylome drives stemness in acute myeloid leukemia |
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| Relations |
| BioProject |
PRJNA765955 |
| SRA |
SRP338572 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE184727_RiboMethSeq_read_count.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE184727_RiboMethSeq_scoreC.txt.gz |
131.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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