Luan et al. 2021 (PRJNA707431)
General Details
| Title | Transcriptome and translatome of ribosomal protein-deficient human cells |
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| Organism | |
| Number of Samples | 102 |
| Release Date | 2021/03/08 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
|---|---|
Repository Details
| SRA | SRP309704 |
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| ENA | SRP309704 |
| GEO | GSE168445 |
| BioProject | PRJNA707431 |
Publication
| Title | |
|---|---|
| Authors | Luan Y,Tang N,Yang J,Liu S,Cheng C,Wang Y,Chen C,Guo YN,Wang H,Zhao W,Zhao Q,Li W,Xiang M,Ju R,Xie Z |
| Journal | Nucleic acids research |
| Publication Date | 2022 Jul 8 |
| Abstract | Human ribosomes have long been thought to be uniform factories with little regulatory function. Accumulating evidence emphasizes the heterogeneity of ribosomal protein (RP) expression in specific cellular functions and development. However, a systematic understanding of functional relevance of RPs is lacking. Here, we surveyed translational and transcriptional changes after individual knockdown of 75 RPs, 44 from the large subunit (60S) and 31 from the small subunit (40S), by Ribo-seq and RNA-seq analyses. Deficiency of individual RPs altered specific subsets of genes transcriptionally and translationally. RP genes were under cotranslational regulation upon ribosomal stress, and deficiency of the 60S RPs and the 40S RPs had opposite effects. RP deficiency altered the expression of genes related to eight major functional classes, including the cell cycle, cellular metabolism, signal transduction and development. 60S RP deficiency led to greater inhibitory effects on cell growth than did 40S RP deficiency, through P53 signaling. Particularly, we showed that eS8/RPS8 deficiency stimulated apoptosis while eL13/RPL13 or eL18/RPL18 deficiency promoted senescence. We also validated the phenotypic impacts of uL5/RPL11 and eL15/RPL15 deficiency on retina development and angiogenesis, respectively. Overall, our study provides a valuable resource for and novel insights into ribosome regulation in cellular activities, development and diseases. © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. |
| PMC | PMC9262593 |
| PMID | 35137207 |
| DOI |
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
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| SRR13884512 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide |  |
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| SRR13884513 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884514 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884515 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884516 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884517 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884518 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884519 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884536 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884537 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884538 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884539 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884540 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884541 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884542 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884543 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884568 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884569 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884570 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884571 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884572 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884573 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884574 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884575 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884544 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884545 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884546 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884547 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884548 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884549 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884550 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884551 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884576 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884577 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884578 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884579 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884580 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884581 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884582 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884583 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884520 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884521 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884522 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884523 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884524 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884525 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884526 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884527 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884552 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884553 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884554 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884555 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884556 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884557 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884558 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884559 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884584 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884585 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884586 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884587 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884588 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884589 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884590 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884591 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884592 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884593 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884594 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884595 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884596 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884597 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884598 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884599 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884528 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884529 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884530 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884531 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884532 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884533 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884534 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884535 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884600 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884601 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884602 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884603 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884604 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884605 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884606 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884607 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884608 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884609 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884610 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884611 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884612 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884613 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884560 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884561 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884562 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884563 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884564 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884565 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884566 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR13884567 | PRJNA707431 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) |
ⓘ For more Information on the columns shown here see: About