Institut for Molekylærbiologi og Genetik

Aarhus Universitets segl

Data

Publicly available NGS data - Human

GSE301785 - Bugai et al., 2026 - DOI: 10.1038/s41586-026-10650-0

  • Cell Lines: HeLa, HCT116
  • Sequencing type: Total RNAseq, Fractionated RNAseq, iCLIP, 3'end-seq
  • Sample set 1: Total RNAseq in HeLa - Control / GANP / LENG8 / ZFC3H1 dTAG-based depletions
  • Sample set 2: Total RNAseq in HeLa - ZFC3H1 dTAG-based depletion +/- ZFC3H1 WT / mutant expression (plasmid-based)
  • Sample set 3: Fractionated RNAseq in HeLa (nucleus / cytoplasm) - Control / GANP / LENG8 / ZFC3H1 dTAG-based depletions
  • Sample set 4: iCLIP in HeLa - UAP56 / LENG8
  • Sample set 5: Fractionated RNAseq in HCT116 (nucleus / cytoplasm) - Control / GANP / LENG8 / ZFC3H1 dTAG-based depletions
  • Sample set 6: 3'end-seq in HeLa - EXOSC3 dTAG-based depletions
  • Sample set 7: Total RNAseq in HeLa - EXOSC3 dTAG-based depletions

 

GSE289428 - Auxillos et al., 2025 - DOI: 10.1093/nar/gkaf240

  • Cell Line: HeLa
  • Sequencing type: True length of diverse capped RNA sequencing (TLDR-seq)
  • Sample: WT

 

GSE279131 - Auxillos et al., 2025 - DOI: 10.1093/nar/gkaf240

  • Cell Line: HeLa
  • Sequencing type: True length of diverse capped RNA sequencing (TLDR-seq)
  • Sample: WT

 

GSE212557 - Polák et al., 2023 - DOI: 10.1016/j.celrep.2023.113325

  • Cell Line: HeLa
  • Sequencing type: RNA-seq
  • Samples: ZFC3H1 depletion (siRNA) + ZFC3H1 WT / mutant expression (plasmid-based)

 

GSE228384 (SuperSeries) - Rouvière et al., 2023 - DOI: 10.1016/j.molcel.2023.05.028 (related to GSE151919)

  • Cell Line: HeLa
  • Sequencing types: RNA-seq (GSE212383) / TT-seq (5min 4sU) (GSE228383)
  • Samples RNA-seq / TT-seq: Control / ARS2 / CPSF73 / INTS11 / EXOSC3 (RRP40) depletion (siRNA)

 

GSE212208 - Rouvière et al., 2023 - DOI: 10.1016/j.molcel.2023.05.028

  • Cell Line: HeLa
  • Sequencing type: RNA-seq
  • Sample set 1: Control / ARS2 depletion (siRNA) + ARS2 WT / mutant expression (plasmid-based)
  • Sample set 2: Control / ARS2 / ZC3H4 depletion (siRNA)
  • Sample set 3: Control / ZC3H18 depletion (dTAG)

 

GSE202980 - Cordiner et al., 2023 - DOI: 10.1038/s41467-023-36345-y

  • Cell Line: HeLa
  • Sequencing type: Temporal iCLIP
  • Samples: ALYREF / CBP20 / CBP80 / RBM7

 

GSE179106 - Gockert et al., 2022 - DOI: 10.1093/nar/gkac001

  • Cell Line: HeLa
  • Sequencing type: RNA 3'end-seq with 4sU labeling (10min)
  • Samples: ZCCHC8 / ZFC3H1 / EXOSC3 (RRP40) depletion (AID) - with/without EPAP treatment

 

GSE151919 - Lykke-Andersen et al., 2021 - DOI: 10.1016/j.molcel.2020.12.014

  • Cell Line: HeLa
  • Sequencing types: RNA-seq / TT-seq (5min 4sU) / RNA 3'end-seq with 4sU labeling (10min)
  • Samples RNA-seq / TT-seq: Control / CPSF73 / INTS11 / EXOSC3 (RRP40) depletion (siRNA)
  • Samples RNA 3'end-seq: Control / INTS11 / EXOSC3 (RRP40) / INTS11xEXOSC3 depletion (siRNA) - with/without EPAP treatment

 

GSE147655 - Wu et al., 2020 - DOI: 10.1093/nar/gkaa594

  • Cell Line: HeLa
  • Sequencing types: TIF-seq / SLIC-CAGE
  • Samples TIF-seq: Control / EXOSC3 (RRP40) depletion (siRNA)
  • Samples SLIC-CAGE: Control / ZFC3H1 / ZCCHC8 depletion (siRNA)

 

GSE148755 - Barra et al., 2020 - DOI: 10.1126/sciadv.aaz9072

  • Cell Line: HeLa
  • Sequencing type: eCLIP
  • Sample: INTS11

 

GSE137612 - Wu et al., 2020 - DOI: 10.1016/j.celrep.2020.01.068

  • Cell Line: HeLa
  • Sequencing type: RNA 3'end-seq total & with 4sU labeling (10min)
  • Samples: Control / RBM7 / EXOSC3 (RRP40) / ZCCHC8 / ZFC3H1 / ZCCHC8xZFC3H1 depletion (siRNA) - with/without EPAP treatment

 

GSE131255 - Silla et al., 2020 - DOI: 10.1093/nar/gkz1238

  • Cell Line: HeLa
  • Sequencing type: RNA-seq
  • Samples: Control / ZC3H3 / RBM26xRBM27 depletion (siRNA)

 

GSE108197 - Silla et al., 2018 - DOI: 10.1016/j.celrep.2018.04.061

  • Cell Line: HeLa
  • Sequencing type: nuclear pA RNA-seq
  • Samples: Control / EXOSC3 (RRP40) depletion (siRNA)

 

GSE99059 - Iasillo et al., 2017 - DOI: 10.1093/nar/gkx647

  • Cell Line: HeLa
  • Sequencing type: RNA-seq
  • Samples: Control / ARS2 / ZC3H18 / CBP80 / NCBP3 depletion (siRNA)

 

GSE99344 - Iasillo et al., 2017 - DOI: 10.1093/nar/gkx647

  • Cell Line: HeLa
  • Sequencing type: ChIP-seq
  • Samples: RNAP II ChIP (and input) in Control / ARS2 / ZC3H18 / EXOSC3 (RRP40) depletion (siRNA)

 

GSE94427 - Giacometti et al., 2017 - DOI: 10.1016/j.celrep.2017.02.046

  • Cell Line: HeLa
  • Sequencing types: RNA-seq / RIP-seq
  • Samples RNAs-seq: Control / PHAX / ZC3H18 depletion (siRNA)
  • Samples RIP-seq: CBP20 / ARS2 / PHAX / ZC3H18

 

GSE84172 - Meola et al., 2016 - DOI: 10.1016/j.molcel.2016.09.025

  • Cell Line: HeLa
  • Sequencing types: RNA-seq / BrU-seq (1h)
  • Samples RNA-seq / BrU-seq: Control / PABPN1 / RBM7 / EXOSC3 (RRP40) / ZCCHC8 / ZFC3H1 depletion (siRNA)

 

GSE75183 - Chen et al., 2016 - DOI: 10.1038/ng.3616

  • Cell Line: HeLa
  • Sequencing type: TIF-seq
  • Samples: Control / ZCCHC8xEXOSC3 depletion (siRNA)

 

SRX365666 / SRX365672 / SRX365673 - Lloret-Llinares et al., 2016 - DOI: 10.1080/15476286.2015.1109769

  • Cell Line: HeLa
  • Sequencing type: RNA-seq
  • Samples: Control / EXOSC3 (RRP40) depletion (siRNA)

 

GSE63791 - Lubas et al., 2015 - DOI: 10.1016/j.celrep.2014.12.026

  • Cell Line: HeLa
  • Sequencing type: iCLIP
  • Samples: RBM7 iCLIP in Control / EXOSC3 (RRP40) depletion (siRNA)

 

GSE63496 - Lubas et al., 2015 - DOI: 10.1016/j.celrep.2014.12.026

  • Cell Line: HeLa
  • Sequencing type: small RNA-seq
  • Samples: Control / EXOSC3 (RRP40) / DIS3xDIS3LxRRP6 depletion (siRNA)

 

GSE57433 - Lykke-Andersen et al., 2014 - DOI: 10.1101/gad.246538.114

  • Cell Line: HEK293 Flp-In T-Rex cells
  • Sequencing types: RNA-seq / 5P-seq / CAGE-seq
  • Samples RNA-seq / 5P-seq: Control / XRN1 / XRN1xSMG6 / XRN1xUPF1 depletion (siRNA)
  • Sample CAGE-seq: WT

 

GSE62047 - Andersson et al., 2014 - DOI: 10.1038/ncomms6336

  • Cell Line: HeLa
  • Sequencing types: CAGE-seq / GRO-seq
  • Samples CAGE-seq: Control / MTREX (MTR4 / SKIV2L2) / EXOSC3 (RRP40) depletion (siRNA)
  • Sample GRO-seq: WT

 

GSE49834 - Andersson et al., 2014 - DOI: 10.1038/nature12787

  • Cell Line: HeLa
  • Sequencing type: CAGE-seq
  • Samples: Control / MTREX (MTR4 / SKIV2L2) depletion (siRNA)

 

GSE48286 - Ntini et al., 2013 - DOI: 10.1038/nsmb.2640

  • Cell Line: HeLa
  • Sequencing type: CAGE-seq / RNA-seq / 3'tag-seq
  • Samples CAGE-seq / RNA-seq: Control / EXOSC3 (RRP40) depletion (siRNA)
  • Sample 3'tag-seq: EXOSC3 (RRP40) depletion (siRNA)

 

GSE29116 - Valen et al., 2011 - DOI: 10.1038/nsmb.2091

  • Cell Line: HeLa
  • Sequencing type: small RNA-seq (two sizes ranges)
  • Samples: Control / EXOSC3 (RRP40) / AGO1xAGO2 / AGO1xAGO2xEXOSC3 / XRN1xXRN2 depletion (siRNA)

Publicly available NGS data - Mouse

GSE279131 - Auxillos et al., 2025 - DOI: 10.1093/nar/gkaf240

  • Cell Line: mESC
  • Sequencing type: True length of diverse capped RNA sequencing (TLDR-seq)
  • Samples: Control / RBM7 / ZCCHC8 depletion (dTAG)

 

GSE271796 - Imamura et al., 2024 - DOI: 10.1016/j.molcel.2024.10.015

  • Cell Line: mESC
  • Sequencing type: small RNA-seq
  • Samples: Control / ZCCHC8 KO

 

GSE178550 - Garland et al., 2022 - DOI: 10.1016/j.molcel.2022.03.004

  • Cell Line: mESC
  • Sequencing type: RNA-seq / RNA 3'end-seq / ChIP-seq
  • Samples RNA-seq: Control / ZCCHC8 KO / ZFC3H1 KO
  • Samples RNA 3'end-seq: Control / ZCCHC8 KO
  • Samples ChIP-seq: MPP8 ChIP (and input) in Control / ZCCHC8 KO

 

GSE137491 - Garland et al., 2019 - DOI: 10.1016/j.celrep.2019.10.011

  • Cell Line: mESC (D0) / Embryonic Bodies (D7)
  • Sequencing type: RNA-seq / ChIP-seq / RIP-seq
  • Samples RNA-seq: Control / ZFC3H1 KO
  • Samples ChIP-seq: H3K4me1 / H3K4me3 / H3K27ac / H3K27me3 / SUZ12 / RPB1 ChIP (and input) in Control / ZFC3H1 KO
  • Samples RIP-seq: SUZ12 / EZH2 RIP (and input) in Control / ZFC3H1 KO

 

GSE115727 (SuperSeries) - Lloret-Llinares et al., 2018 - DOI: 10.1093/nar/gky817

Publicly available NGS data - Yeast (S. cerevisiae)

PRJEB39819 / PRJEB33089 / PRJEB40892 / PRJEB40438 / PRJEB46704 / ERS5465447 - Tudek et al., 2021 - DOI: 10.1038/s41467-021-25251-w

  • Background: W303
  • Sequencing type: Nanopore direct pA RNA sequencing (Oxford Nanopore Technologies)
  • Samples set 1: Control / Rrp6 / Trf4 / Trf5 / Ski2 / Ccr4 / Pan2 / Mtf1 depletion (Δ) - with/without Pap1 mutation
  • Samples set 2: Mex67-AnchorAway - with/without Rapamicin (15min) - 25/38ºC
  • Samples set 3: Dis3-AnchorAway / Dis3-AnchorAway Rrp6-AnchorAway
  • Warning: Samples are combined with unrelated samples from independent species - Refer to manuscript for individual samples number

 

PRJEB41964 / PRJEB45063 / PRJEB41965 / PRJEB41543 / PRJEB46679 / PRJEB46684 / PRJEB46685 - Turtola et al., 2021 - DOI: 10.1101/gad.348634.121

  • Background: W303
  • Sequencing type: Nanopore direct pA RNA sequencing (Oxford Nanopore Technologies)
  • Samples: Mex67-AnchorAway - with/without Rapamicin (15min) - with/without Nab2 / Pab1 overexpression  - with/without pab1 mutant - wit/without 4tU (15min)
  • Warning: Samples are combined with unrelated Humain / Mouse samples - Refer to manuscript for individual samples number

 

GSE108550 - Schmid et al., 2018 - DOI: 10.1016/j.celrep.2018.07.104

  • Background: W303
  • Sequencing type: RNA 3'end-seq total & with 4tU labeling (2min)
  • Samples: Nab2-AnchorAway / Mex67-AnchorAway - with/without Rapamicin (15min) - with/without EPAP treatment

 

GSE108477 - Tudek et al., 2018 - DOI: 10.1016/j.celrep.2018.07.103

  • Background: W303
  • Sequencing type: RNA 3'end-seq total & with 4tU labeling (2min)
  • Samples: Nab2-AnchorAway / Mex67-AnchorAway - with/without Rapamicin (15min) - with EPAP treatment

 

GSE65001 - Schmid et al., 2015 - DOI: 10.1016/j.celrep.2015.06.008

  • Background: W303
  • Sequencing type: RNA-seq
  • Samples: Control / Nab2-AnchorAway - with/without Rapamicin (15/30min)

Bioinformatic tools

seqNdisplayR

 

A computational tool for easy generation of customizable and reproducible plots of sequencing coverage data (Tutorial)

Revideret 18.06.2026