GEO and SRA links

  • 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)