PAXT/NEXT targeting of RNA exosome regulates antisense transcripts through cohesin-mediated long-range contacts [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 13 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Samples
- 13 samples: 13 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
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.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE154083_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
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 PRJNA645085 and SRA study SRP271085. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 13 sample titles: 13 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.
- GSM4663648 HeLa cells MTR4 IP
- GSM4663649 HeLa cells Input MTR4 IP
- GSM4663650 HeLa cells ZFC3H1 IP
- GSM4663651 HeLa cells input ZFC3H1/CTCF IP
- GSM4663652 HeLa cells ZCCHC8 IP
- GSM4663653 HeLa cells input ZCCHC8 IP
- GSM4663654 HeLa cells CTCF IP
- GSM4663655 HeLa cells shControl RAD21 IP
- GSM4663656 HeLa cells input sh Control
- GSM4663657 HeLa cells sh MTR4 RAD21 IP
- GSM4663658 HeLa cells input shMTR4 IP
- GSM4663659 HeLa cells shZFC3H1 RAD21 IP
- GSM4663660 HeLa cells input shZFC3H1 IP
- GSE154100 PAXT/NEXT targeting of RNA exosome regulates antisense transcripts through cohesin-mediated long-range contacts 17 samples shares paxt, next, cohesin-mediated, transcripts, long-range, targeting, antisense, contacts
- GSE342032 Isoform-selective antisense oligonucleotide knockdown of SNCA-dIRE and SNCA-IRE transcripts in SK-MEL-28 cells (dose-response) 36 samples shares transcripts, antisense
- GSE300872 Investigations into the biological activity of avobenzone as part of a Next Generation Risk Assessment 328 samples shares next
- GSE305968 Integrative single-cell analysis reveals malignant archetypes and proliferative hierarchies in multiple myeloma [Part 2 of 4: Illumina NextSeq 500; MARS] 267 samples shares next
- GSE255626 Next generation sequencing from primary glioblastoma patient tissues (Total RNA-seq) 109 samples shares next
- GSE295024 Imlunestrant: A next-generation oral SERD overcomes ESR1 mutant resistance in estrogen receptor-positive breast cancer 72 samples shares next
- GSE319124 Next-GenerationPediatric Cancer Models: Patient-Matched Orthotopic Xenografts, 3D Organoids, 2D Cultures, and Cell Lines for Identification of Therapeutic Vulnerabilities in Pediatric Solid Tumors [scRNAseq] 59 samples shares next
- GSE299096 Oligo-CALL: A Next-Generation Barcoding Platform for Studying Resistance to Targeted Therapy [bulk RNA-seq] 48 samples shares next
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.