Lykke-Andersen S, Žumer K, Molska EŠ, Rouvière JO, Wu G, Demel C, Schwalb B, Schmid M, Cramer P, Jensen TH. Integrator is a genome-wide attenuator of non-productive transcription. Mol. Cell 2021 Feb 4. GSE151919 (RNAseq and TTseq of HeLa siRRP40, siCPSF73, siINTS11; RNA 3'end-seq for siINTS11 and siRRP40)
Wu M, Karadoulama E, Lloret-Llinares M, Rouviere JO, Vaagensø CS, Moravec M, Li B, Wang J, Wu G, Gockert M, Pelechano V,Jensen TH, Sandelin A. The RNA exosome shapes the expression of key protein-coding genes. Nucleic Acids Res. 2020 Sept 4. GSE147655 (TIFseq from HeLa siRRP40 and ctrl; SLICCAGE from HeLa siZCCHC8 and siZFC3H1) ,
Barra J, Gaidosh GS, Blumenthal E, Beckedorff F, Tayari MM, Kirstein N, Karakach TK, Jensen TH, Impens F, Gevaert K, Leucci E, Shiekhattar R, Marine JC. Integrator restrains paraspeckles assembly by promoting isoform switching of the lncRNA NEAT1.Science Adv. 2020 Jul. GSE148755 (eCLIP of INTS11)
Wu G, Schmid M, Rib L, Polak P, Meola N, Sandelin A, Jensen TH. A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome.Cell Rep. 2020 Feb 18. GSE137612 (RNA 3'seq +/-EPAP treatment and +/- 4sU IP of HeLa siRRP40, siZCCHC8, siZFC3H1 and siZCCHC8/siZFC3H1)
Silla T, Schmid M, Dou Y, Garland W, Milek M, Imami K, Johnsen D, Polak P, Andersen JS, Selbach M, Landthaler M, Jensen TH.The human ZC3H3 and RBM26/27 proteins are critical for PAXT-mediated nuclear RNA decay.Nucleic Acids Res. 2020 Mar 18. GSE131255 (RNAseq of siZC3H3 and siRBM26/siRBM27)
Garland W, Comet I, Wu M, Radzisheuskaya A, Rib L, Vitting-Seerup K, Lloret-Llinares M, Sandelin A, Helin K, Jensen TH. A Functional Link between Nuclear RNA Decay and Transcriptional Control Mediated by the Polycomb Repressive Complex 2. Cell Reports 2019 Nov 12. GSE137491 (RNAseq of mouse ES cell ctrl and zfc3h1 knock-out, ChIPseq and RIP of PRC components in the same cells)
Lloret-Llinares M, Karadoulama E, Chen Y, Wojenski L, Villafano G, Bornhold-Lange J, Andersson R, Core L, Sandelin A, Jensen TH. The RNA exosome contributes to gene expression regulation during stem cell differentiation.Nucleic Acids Res. 2018 Sept 13. GSE115727 (CAGE, RNAseq and PROseq of mouse ES cells, ctrl and RRP40 knock-down) GSE118043 (CAGE of mouse ES cells and RBM7 knock-down) GSE118052 (PROseq of mouse ES cells and RBM7 knock-down) GSE118054 (RNAseq of mouse ES cells and embryoid bodies with RBM7 knock-down)
Schmid M, Tudek A, Jensen TH. Simultaneous Measurement of Transcriptional and Post-transcriptional Parameters by 3' End RNA-Seq.Cell Reports 2018 Aug 28 GSE108550 (RNA 3'end seq S. cerevisiae +/-EPAP and 4tU labelling)
Tudek A, Schmid M, Makaras M, Barrass JD, Beggs JD, Jensen TH. A Nuclear Export Block Triggers the Decay of Newly Synthesized Polyadenylated RNA.Cell Reports 2018 Aug 28 GSE108477 (RNA 3'end seq S. cerevisiae Nab2 and Mex67-anchor away, +/-EPAP and 4tU labelling)
Silla T, Karadoulama E, Mąkosa D, Lubas M, Jensen TH. The RNA Exosome Adaptor ZFC3H1 Functionally Competes with Nuclear Export Activity to Retain Target Transcripts.Cell Reports 2018 May 15 GSE108197
Iasillo C, Schmid M, Yahia Y, Maqbool MA, Descostes N, Karadoulama E, Bertrand E, Andrau JC, Jensen TH. ARS2 is a general suppressor of pervasive transcription.NAR 2017 July 24 (RNA-seq data (HeLa, siARS2, siZC3H18 and siCBP80, and siEGFP): GSE99059. ChIP-seq data (HeLa, siARS2, siZC3H18 and siRRP40, and siFFL): GSE99344.)
Giacometti S, Benbahouche NE, Domanski M, Robert MC, Meola N, Lubas M, Bukenborg J, Andersen JS, Schulze WM, Verheggen C, Kudla G, Jensen TH, Bertrand E. Mutually Exclusive CBC-Containing Complexes Contribute to RNA Fate.Cell Reports 2017 Mar 14 (RNA-seq data (HeLa, siPHAX, siZC3H18 and control siRNAs) and iCLIP data (CBP20, ARS2, PHAX, and ZC3H18 proteins in HeLa and HEK293 cells): GSE94427
Meola M, Domanski M, Karadoulama E, Chen Y, Gentil C, Pultz D, Vitting-Seerup K, Lykke-Andersen S, Andersen JS, Sandelin A and Jensen TH. Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts. Mol Cell. Dec 2016. GSE84172 (RNAseq of total RNA and 1h BrU labelled RNA in control, RRP40, RBM7, ZCCHC8, ZFC3H1 and PABPN1 KD)
Chen Y, Pai AA, Herudek J, Lubas M, Meola N, Järvelin AI, Andersson R, Pelechano V, Steinmetz LM, Jensen TH, Sandelin A. Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters. Nat Genet. 2016 Jul 25. GSE75183 (TIFseq in control and RRP40 ZCCHC8 KD)
Lloret-Llinares M, Mapendano CK, Martlev LH, Lykke-Andersen S, Jensen TH. Relationships between PROMPT and gene expression. RNA Biol. 2015 Nov 17:0. SRA:SRX365666, SRA:SRX365672 and SRA:SRX365673 (RNAseq in RRP40 KD cells)
Schmid M, Olszewski P, Pelechano V, Gupta I, Steinmetz LM, Jensen TH. The Nuclear PolyA-Binding Protein Nab2p Is Essential for mRNA Production. Cell Reports. 2015 Jun 24. GEO:GSE65001 (RNAseq after nuclear Nab2p depletion)
Lubas M, Andersen PR, Schein A, Dziembowski A, Kudla G, Jensen TH. The human nuclear exosome targeting complex is loaded onto newly synthesized RNA to direct early ribonucleolysis. Cell Reports. 2015 Jan 13;10(2):178-92. GEO:GSE63791 (RBM7 iCLIP in control and RRP40 KD)
Lykke-Andersen S, Chen Y, Ardal BR, Lilje B, Waage J, Sandelin A, Jensen TH. Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes. Genes Dev. 2014 Nov 15;28(22):2498-517. GEO:GSE57433 (RNAseq and 5'end-seq in control, XRN1 and NMD factor KDs)
Andersson R, Refsing Andersen P, Valen E, Core LJ, Bornholdt J, Boyd M, Heick Jensen T, Sandelin A. Nuclear stability and transcriptional directionality separate functionally distinct RNA species. Nat Commun. 2014 Nov 12;5:5336. GEO:GSE62047 (CAGE in control, MTR4 and RRP40 KDs, GROseq HeLa)
