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| Status |
Public on Jun 28, 2019 |
| Title |
Effects of transcription on genome - nuclear lamina interactions: DamID-seq data |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Other
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| Summary |
In mammalian nuclei, transcriptionally active genomic regions tend to localize to the interior of the nucleus while inactive regions are often located at at the nuclear lamina. In this study we activated specific genes in lamina-associated domains by TALE-VP64 or CRISPRa-mediated activation. We also reduced transcription of individual genes by knockout of promoter/enhancer regions, or by insertion of a transcription termination sequence. In each case we generated genome-wide DamID maps to determine changes in nuclear lamina interactions, and in selected cases we also generated Repli-seq maps and/or RNAseq data.
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| Overall design |
Transcription was locally manipulated in mouse and human cell lines by using several techniques: random integration of a hPGK-EGFP expression cassette, TALE-VP64, CRISPRa, deletion of endogenous gene promoters or truncation of an endogenous transcript. Changes in 3D genome architecture were assesses by mapping lamina interaction with DamID.
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| Contributor(s) |
Brueckner L, van Schaik T, Peric-Hupkes D, Leemans C, Sima J, Zhao PA, Gilbert DM, van Steensel B |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jun 25, 2019 |
| Last update date |
Jun 30, 2019 |
| Contact name |
Bas van Steensel |
| E-mail(s) |
b.v.steensel@nki.nl
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| Phone |
+ 31 20 512 2040
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| Fax |
+31 20 669 1383
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| URL |
http://www.nki.nl/nkidep/vansteensel
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| Organization name |
Netherlands Cancer Institute
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| Department |
division of Molecular Biology
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| Lab |
van Steensel group
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| Street address |
Plesmanlaan 121
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| City |
Amsterdam |
| ZIP/Postal code |
1066 CX |
| Country |
Netherlands |
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| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (130)
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| GSM3904474 |
DamID, Dam, F121-9 clone CM1417, rep4 |
| GSM3904475 |
DamID, Dam, F121-9 clone CM1420, rep1 |
| GSM3904476 |
DamID, Dam, F121-9 clone CM1420, rep2 |
| GSM3904477 |
DamID, Dam, F121-9 clone CM1420, rep3 |
| GSM3904478 |
DamID, Dam, F121-9 clone CM1420, rep4 |
| GSM3904479 |
DamID, Dam, F121-9, TALE-VP64, Nrp1, rep1 |
| GSM3904480 |
DamID, Dam, F121-9, TALE-VP64, Nrp1, rep2 |
| GSM3904481 |
DamID, Dam, F121-9, TALE-VP64, Sox6, rep1 |
| GSM3904482 |
DamID, Dam, F121-9, TALE-VP64, Sox6, rep2 |
| GSM3904483 |
DamID, Dam, RPE, CRISPRa, control, rep1 |
| GSM3904484 |
DamID, Dam, RPE, CRISPRa, control, rep2 |
| GSM3904485 |
DamID, Dam, RPE, CRISPRa, ABCB1, rep1 |
| GSM3904486 |
DamID, Dam, RPE, CRISPRa, ABCB1, rep2 |
| GSM3904487 |
DamID, Dam, RPE, CRISPRa, ADAM22, rep1 |
| GSM3904488 |
DamID, Dam, RPE, CRISPRa, ADAM22, rep2 |
| GSM3904489 |
DamID, Dam, RPE, CRISPRa, CCSER1, rep1 |
| GSM3904490 |
DamID, Dam, RPE, CRISPRa, CCSER1, rep2 |
| GSM3904491 |
DamID, Dam, RPE, CRISPRa, GRID2, rep1 |
| GSM3904492 |
DamID, Dam, RPE, CRISPRa, GRID2, rep2 |
| GSM3904493 |
DamID, Dam, RPE, CRISPRa, KIAA1804, rep1 |
| GSM3904494 |
DamID, Dam, RPE, CRISPRa, KIAA1804, rep2 |
| GSM3904495 |
DamID, Dam, RPE, CRISPRa, NLGN1, rep1 |
| GSM3904496 |
DamID, Dam, RPE, CRISPRa, NLGN1, rep2 |
| GSM3904497 |
DamID, Dam, RPE, CRISPRa, PCNX2, rep1 |
| GSM3904498 |
DamID, Dam, RPE, CRISPRa, PCNX2, rep2 |
| GSM3904499 |
DamID, Dam, RPE, CRISPRa, PTN, rep1 |
| GSM3904500 |
DamID, Dam, RPE, CRISPRa, PTN, rep2 |
| GSM3904501 |
DamID, Dam, RPE, CRISPRa, SLC35F3, rep1 |
| GSM3904502 |
DamID, Dam, RPE, CRISPRa, SOX6, rep1 |
| GSM3904503 |
DamID, Dam, RPE, CRISPRa, SOX6, rep2 |
| GSM3904504 |
DamID, Dam, RPE, CRISPRa, TRAM1L1, rep1 |
| GSM3904505 |
DamID, Dam, RPE, CRISPRa, TRAM1L1, rep2 |
| GSM3904506 |
DamID, Dam, RPE, CRISPRa, ZNF804B, rep1 |
| GSM3904507 |
DamID, Dam, RPE, CRISPRa, ZNF804B, rep2 |
| GSM3904508 |
DamID, Dam, RPE, CRISPRa, CCSER1+GRID2, rep1 |
| GSM3904509 |
DamID, Dam, RPE, CRISPRa, CCSER1+GRID2, rep2 |
| GSM3904510 |
DamID, Dam, RPE, CRISPRa, ABCB4+ABCB1+ADAM22+RUNDC3B, rep1 |
| GSM3904511 |
DamID, Dam, RPE, CRISPRa, ABCB4+ABCB1+ADAM22+RUNDC3B, rep2 |
| GSM3904512 |
DamID, Dam, F121-9, Morc1 Cdel, cloneA6, rep1 |
| GSM3904513 |
DamID, Dam, F121-9, Morc1 Cdel, cloneA6, rep2 |
| GSM3904514 |
DamID, Dam, F121-9, Morc1 Cdel, cloneA6, rep3 |
| GSM3904515 |
DamID, Dam, F121-9, Morc1 Cdel, cloneA6, rep4 |
| GSM3904516 |
DamID, Dam, F121-9, Morc1 Cdel, cloneE2, rep1 |
| GSM3904517 |
DamID, Dam, F121-9, Morc1 Cdel, cloneE2, rep2 |
| GSM3904518 |
DamID, Dam, F121-9, Morc1 Cdel, cloneE2, rep3 |
| GSM3904519 |
DamID, Dam, F121-9, Morc1 Cdel, cloneE2, rep4 |
| GSM3904520 |
DamID, Dam, F121-9, Morc1 ABCdel, cloneA12, rep1 |
| GSM3904521 |
DamID, Dam, F121-9, Morc1 ABCdel, cloneA12, rep2 |
| GSM3904522 |
DamID, Dam, F121-9, Morc1 ABCdel, cloneA12, rep3 |
| GSM3904523 |
DamID, Dam, F121-9, Morc1 ABCdel, cloneA12, rep4 |
| GSM3904524 |
DamID, Dam, F121-9, Morc1 ABCdel, cloneB11, rep1 |
| GSM3904525 |
DamID, Dam, F121-9, Morc1 ABCdel, cloneB11, rep2 |
| GSM3904526 |
DamID, Dam, F121-9, Morc1 ABCdel, cloneB11, rep3 |
| GSM3904527 |
DamID, Dam, F121-9, Morc1 ABCdel, cloneB11, rep4 |
| GSM3904528 |
DamID, Dam, F121-9, PASins Cobl, rep1 |
| GSM3904529 |
DamID, Dam, F121-9, PASins Cobl, rep2 |
| GSM3904530 |
DamID, Dam, F121-9, PASins Cobl, rep3 |
| GSM3904531 |
DamID, Dam, F121-9, PASins Cobl, rep4 |
| GSM3904532 |
DamID, Dam, F121-9, PASins Cobl, rep5 |
| GSM3904533 |
DamID, Dam, F121-9, PASins Cobl, rep6 |
| GSM3904534 |
DamID, Dam, F121-9, PASins Cobl, rep7 |
| GSM3904535 |
DamID, Dam, F121-9, PASins Cobl, rep8 |
| GSM3904536 |
DamID, Dam-LMNB1, F121-9 clone CM1417, rep1 |
| GSM3904537 |
DamID, Dam-LMNB1, F121-9 clone CM1417, rep2 |
| GSM3904538 |
DamID, Dam-LMNB1, F121-9 clone CM1417, rep3 |
| GSM3904539 |
DamID, Dam-LMNB1, F121-9 clone CM1417, rep4 |
| GSM3904540 |
DamID, Dam-LMNB1, F121-9 clone CM1420, rep1 |
| GSM3904541 |
DamID, Dam-LMNB1, F121-9 clone CM1420, rep2 |
| GSM3904542 |
DamID, Dam-LMNB1, F121-9 clone CM1420, rep3 |
| GSM3904543 |
DamID, Dam-LMNB1, F121-9 clone CM1420, rep4 |
| GSM3904544 |
DamID, Dam-LMNB1, F121-9, TALE-VP64, Nrp1, rep1 |
| GSM3904545 |
DamID, Dam-LMNB1, F121-9, TALE-VP64, Nrp1, rep2 |
| GSM3904546 |
DamID, Dam-LMNB1, F121-9, TALE-VP64, Sox6, rep1 |
| GSM3904547 |
DamID, Dam-LMNB1, F121-9, TALE-VP64, Sox6, rep2 |
| GSM3904548 |
DamID, Dam-LMNB1, RPE, CRISPRa, control, rep1 |
| GSM3904549 |
DamID, Dam-LMNB1, RPE, CRISPRa, control, rep2 |
| GSM3904550 |
DamID, Dam-LMNB1, RPE, CRISPRa, ABCB1, rep1 |
| GSM3904551 |
DamID, Dam-LMNB1, RPE, CRISPRa, ABCB1, rep2 |
| GSM3904552 |
DamID, Dam-LMNB1, RPE, CRISPRa, ADAM22, rep1 |
| GSM3904553 |
DamID, Dam-LMNB1, RPE, CRISPRa, ADAM22, rep2 |
| GSM3904554 |
DamID, Dam-LMNB1, RPE, CRISPRa, CCSER1, rep1 |
| GSM3904555 |
DamID, Dam-LMNB1, RPE, CRISPRa, CCSER1, rep2 |
| GSM3904556 |
DamID, Dam-LMNB1, RPE, CRISPRa, GRID2, rep1 |
| GSM3904557 |
DamID, Dam-LMNB1, RPE, CRISPRa, GRID2, rep2 |
| GSM3904558 |
DamID, Dam-LMNB1, RPE, CRISPRa, KIAA1804, rep1 |
| GSM3904559 |
DamID, Dam-LMNB1, RPE, CRISPRa, KIAA1804, rep2 |
| GSM3904560 |
DamID, Dam-LMNB1, RPE, CRISPRa, NLGN1, rep1 |
| GSM3904561 |
DamID, Dam-LMNB1, RPE, CRISPRa, NLGN1, rep2 |
| GSM3904562 |
DamID, Dam-LMNB1, RPE, CRISPRa, PCNX2, rep1 |
| GSM3904563 |
DamID, Dam-LMNB1, RPE, CRISPRa, PCNX2, rep2 |
| GSM3904564 |
DamID, Dam-LMNB1, RPE, CRISPRa, PTN, rep1 |
| GSM3904565 |
DamID, Dam-LMNB1, RPE, CRISPRa, PTN, rep2 |
| GSM3904566 |
DamID, Dam-LMNB1, RPE, CRISPRa, SLC35F3, rep1 |
| GSM3904567 |
DamID, Dam-LMNB1, RPE, CRISPRa, SOX6, rep1 |
| GSM3904568 |
DamID, Dam-LMNB1, RPE, CRISPRa, SOX6, rep2 |
| GSM3904569 |
DamID, Dam-LMNB1, RPE, CRISPRa, TRAM1L1, rep1 |
| GSM3904570 |
DamID, Dam-LMNB1, RPE, CRISPRa, TRAM1L1, rep2 |
| GSM3904571 |
DamID, Dam-LMNB1, RPE, CRISPRa, ZNF804B, rep1 |
| GSM3904572 |
DamID, Dam-LMNB1, RPE, CRISPRa, ZNF804B, rep2 |
| GSM3904573 |
DamID, Dam-LMNB1, RPE, CRISPRa, CCSER1+GRID2, rep1 |
| GSM3904574 |
DamID, Dam-LMNB1, RPE, CRISPRa, CCSER1+GRID2, rep2 |
| GSM3904575 |
DamID, Dam-LMNB1, RPE, CRISPRa, ABCB4+ABCB1+ADAM22+RUNDC3B, rep1 |
| GSM3904576 |
DamID, Dam-LMNB1, RPE, CRISPRa, ABCB4+ABCB1+ADAM22+RUNDC3B, rep2 |
| GSM3904577 |
DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneA6, rep1 |
| GSM3904578 |
DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneA6, rep2 |
| GSM3904579 |
DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneA6, rep3 |
| GSM3904580 |
DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneA6, rep4 |
| GSM3904581 |
DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneE2, rep1 |
| GSM3904582 |
DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneE2, rep2 |
| GSM3904583 |
DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneE2, rep3 |
| GSM3904584 |
DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneE2, rep4 |
| GSM3904585 |
DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneA12, rep1 |
| GSM3904586 |
DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneA12, rep2 |
| GSM3904587 |
DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneA12, rep3 |
| GSM3904588 |
DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneA12, rep4 |
| GSM3904589 |
DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneB11, rep1 |
| GSM3904590 |
DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneB11, rep2 |
| GSM3904591 |
DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneB11, rep3 |
| GSM3904592 |
DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneB11, rep4 |
| GSM3904593 |
DamID, Dam-LMNB1, F121-9, PASins Cobl, rep1 |
| GSM3904594 |
DamID, Dam-LMNB1, F121-9, PASins Cobl, rep2 |
| GSM3904595 |
DamID, Dam-LMNB1, F121-9, PASins Cobl, rep3 |
| GSM3904596 |
DamID, Dam-LMNB1, F121-9, PASins Cobl, rep4 |
| GSM3904597 |
DamID, Dam-LMNB1, F121-9, PASins Cobl, rep5 |
| GSM3904598 |
DamID, Dam-LMNB1, F121-9, PASins Cobl, rep6 |
| GSM3904599 |
DamID, Dam-LMNB1, F121-9, PASins Cobl, rep7 |
| GSM3904600 |
DamID, Dam-LMNB1, F121-9, PASins Cobl, rep8 |
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| This SubSeries is part of SuperSeries: |
| GSE133275 |
Effects of transcription on genome - nuclear lamina interactions |
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| Relations |
| BioProject |
PRJNA551544 |
| SRA |
SRP212317 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE133272_RAW.tar |
8.1 Gb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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