Senescent cells cluster CTCF on nuclear speckles to sustain their splicing program

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1197538 and SRA study SRP513939. Searching any of these in the dataset finder brings you back here.

How we read this: Read from 34 sample titles: 26 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

• GSM8328987 IMR90, wild type, RNA-seq, replicate 1
• GSM8328988 IMR90, wild type, RNA-seq, replicate 2
• GSM8328989 IMR90, siHMGB2, RNA-seq, replicate 1
• GSM8328990 IMR90, siHMGB2, RNA-seq, replicate 2
• GSM8328991 IMR90, ICM, RNA-seq, replicate 1
• GSM8328992 IMR90, ICM, RNA-seq, replicate 2
• GSM8328993 IMR90, siSRRM2, RNA-seq, replicate 1
• GSM8328994 IMR90, siSRRM2, RNA-seq, replicate 2
• GSM8328995 IMR90, siBANF1, RNA-seq, replicate 1
• GSM8328996 IMR90, siBANF1, RNA-seq, replicate 2
• GSM8328997 IMR90, wild type, replicate 1, eclip
• GSM8328998 IMR90, wild type, replicate 2, eclip
• GSM8328999 IMR90, ICM, replicate 1, eclip
• GSM8329000 IMR90, ICM, replicate 2, eclip
• GSM8329001 IMR90, wild type, replicate 1, input
• GSM8329002 IMR90, wild type, replicate 2, input
• GSM8329003 IMR90, ICM, replicate 1, input
• GSM8329004 IMR90, ICM, replicate 2, input
• GSM8329005 SON_Control
• GSM8329006 SON_D3
• GSM8329007 SON_D6
• GSM8329008 HMGB2
• GSM8329009 HMGB2_Input
• GSM8607128 IMR90, ICM, replicate 3
• GSM8607129 IMR90, ICM, replicate 4
• GSM8607130 IMR90, siCTCF, replicate 1
• GSM8607131 IMR90, siCTCF, replicate 2
• GSM8669512 p1492s3_Prol_SRSF7_H2O2_Papantonis
• GSM8669513 p1492s5_ICM_SRSF7_H2O2_Papantonis
• GSM8669514 p1492s2_Prol_NLS_control_Papantonis
• GSM8669515 p1492s6_ICM_SRSF7_control_Papantonis
• GSM8669516 p1492s4_Prol_SRSF7_control_Papantonis
• GSM8669517 p1492s1_Prol_NLS_H2O2_Papantonis
• GSM9510394 HMGB2_DSG-whole

• GSE217753 DNA methylation insulates exons from CTCF loops with nuclear speckles (CUT&TAG) 14 samples shares ctcf, speckles, nuclear
• GSE285077 Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles [RNA-seq] 76 samples shares speckles, splicing, nuclear
• GSE285088 Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles [eCLIP-seq] 24 samples shares speckles, splicing, nuclear
• GSE239270 Investigate FOXA2, NKX2-1, CTCF and P300 cistrome and enhancer (H3K27ac and H3k4me1) reprogramming during NEPC transformation by ChIP-seq. 104 samples shares ctcf, program
• GSE248102 CTCF/cohesin organize the ground state of chromatin-nuclear speckle association [RNA-Seq] 59 samples shares ctcf, nuclear
• GSE341599 CTCFL(BORIS) contributes to the transcriptional program of ovarian cancer by relaxing CTCF-mediated three-dimensional genome organization 32 samples shares ctcf, program
• GSE216843 Hypoxia-induced CTCF mediates alternative splicing via coupling chromatin looping and RNA Pol II pause to promote EMT in breast cancer 18 samples shares ctcf, splicing
• GSE288172 Influence of NIPBL Knockdown-Induced Alterations in Cohesin Loop Extrusion on CTCF Loops, Enhancer-Promoter Connectivity, and PRC Domain Contacts During hESC Differentiation into Pancreatic Lineages 263 samples shares ctcf

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