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Series GSE133272 Query DataSets for GSE133272
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
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.
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.
Contributor(s) Brueckner L, van Schaik T, Peric-Hupkes D, Leemans C, Sima J, Zhao PA, Gilbert DM, van Steensel B
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Submission date Jun 25, 2019
Last update date Jun 30, 2019
Contact name Bas van Steensel
Phone + 31 20 512 2040
Fax +31 20 669 1383
Organization name Netherlands Cancer Institute
Department division of Molecular Biology
Lab van Steensel group
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066 CX
Country Netherlands
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (130)
GSM3904471 DamID, Dam, F121-9 clone CM1417, rep1
GSM3904472 DamID, Dam, F121-9 clone CM1417, rep2
GSM3904473 DamID, Dam, F121-9 clone CM1417, rep3
This SubSeries is part of SuperSeries:
GSE133275 Effects of transcription on genome - nuclear lamina interactions
BioProject PRJNA551544
SRA SRP212317

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Supplementary file Size Download File type/resource
GSE133272_RAW.tar 8.1 Gb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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