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| Status |
Public on Jun 28, 2019 |
| Title |
Effects of transcription on genome - nuclear lamina interactions: RNA-seq data |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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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 of individual genes was manipulated in human RPE-1 cells by CRISPRa. Changes in gene expression were assayed by RNA-seq.
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| Contributor(s) |
Brueckner L, 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 (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (20)
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| GSM3904601 |
RNA-seq, RPE, CRISPRa, ctrl, rep1 [4861_1_CM1502_CGATGTA] |
| GSM3904602 |
RNA-seq, RPE, CRISPRa, ctrl, rep2 [4862_1_CM1502_ATCACGA] |
| GSM3904603 |
RNA-seq, RPE, CRISPRa, ABCB1, rep1 [4861_9_plb186_ATGTCAG] |
| GSM3904604 |
RNA-seq, RPE, CRISPRa, ABCB1, rep2 [4862_9_plb186_CGTACGT] |
| GSM3904605 |
RNA-seq, RPE, CRISPRa, ADAM22, rep1 [4861_10_plb187_CCGTCCC] |
| GSM3904606 |
RNA-seq, RPE, CRISPRa, ADAM22, rep2 [4862_10_plb187_GAGTGGA] |
| GSM3904607 |
RNA-seq, RPE, CRISPRa, CCSER1, rep1 [4861_5_plb170_CAGATCA] |
| GSM3904608 |
RNA-seq, RPE, CRISPRa, CCSER1, rep2 [4862_5_plb170_TAGCTTA] |
| GSM3904609 |
RNA-seq, RPE, CRISPRa, GRID2, rep1 [4861_6_plb171_CTTGTAA] |
| GSM3904610 |
RNA-seq, RPE, CRISPRa, GRID2, rep2 [4862_6_plb171_GGCTACA] |
| GSM3904611 |
RNA-seq, RPE, CRISPRa, MLK4, rep1 [4861_8_plb182_AGTTCCG] |
| GSM3904612 |
RNA-seq, RPE, CRISPRa, MLK4, rep2 [4862_8_plb182_GTTTCGG] |
| GSM3904613 |
RNA-seq, RPE, CRISPRa, PCNX2, rep1 [4861_7_plb181_AGTCAAC] |
| GSM3904614 |
RNA-seq, RPE, CRISPRa, PCNX2, rep2 [4862_7_plb181_GTGGCCT] |
| GSM3904615 |
RNA-seq, RPE, CRISPRa, PTN, rep1 [4861_3_plb162_ACAGTGA] |
| GSM3904616 |
RNA-seq, RPE, CRISPRa, PTN, rep2 [4862_3_plb162_ACTTGAA] |
| GSM3904617 |
RNA-seq, RPE, CRISPRa, SOX6, rep1 [4861_4_plb163_GCCAATA] |
| GSM3904618 |
RNA-seq, RPE, CRISPRa, SOX6, rep2 [4862_4_plb163_GATCAGA] |
| GSM3904619 |
RNA-seq, RPE, CRISPRa, ABCB4+ABCB1+ADAM22+RUNDC3B, rep1 [4861_11_plb184_3_GTCCGCA] |
| GSM3904620 |
RNA-seq, RPE, CRISPRa, ABCB4+ABCB1+ADAM22+RUNDC3B, rep2 [4862_11_plb184_3_ACTGATA] |
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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 |
PRJNA551545 |
| SRA |
SRP212318 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE133273_RNAseq_CRISPRa_RPE_readcounts_BvS190614.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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