U4 inhibits premature cleavage and polyadenylation of pre-mRNAs
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 42 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
- Mus musculus (mouse)
- Samples
- 42 samples: 42 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.
- Paper
- U4 snRNP inhibits premature cleavage and polyadenylation of pre-mRNAsProceedings of the National Academy of Sciences of the United States of America · 2024
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 GSE262385_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 PRJNA1091625 and SRA study SRP497696. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 30 samples read as cases, 6 as controls.
How we read this: Read from 42 sample titles: 42 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.
- GSM8164215 HeLa cells, NC AMO treated, repeat 1 (RNA-seq)
- GSM8164216 HeLa cells, NC AMO treated, repeat 2 (RNA-seq)
- GSM8164217 HeLa cells, U1 AMO treated, repeat 1 (RNA-seq)
- GSM8164218 HeLa cells, U1 AMO treated, repeat 2 (RNA-seq)
- GSM8164219 HeLa cells, U4 AMO treated, repeat 1 (RNA-seq)
- GSM8164220 HeLa cells, U4 AMO treated, repeat 2 (RNA-seq)
- GSM8164233 HeLa cells, NC AMO treated, repeat 1 (3'-Seq)
- GSM8164234 HeLa cells, NC AMO treated, repeat 2 (3'-Seq)
- GSM8164235 HeLa cells, U1 AMO treated, repeat 1 (3'-Seq)
- GSM8164236 HeLa cells, U1 AMO treated, repeat 2 (3'-Seq)
- GSM8164237 HeLa cells, U4 AMO treated, repeat 1 (3'-Seq)
- GSM8164238 HeLa cells, U4 AMO treated, repeat 2 (3'-Seq)
- GSM8164239 NIH-3T3 cells, NC AMO treated, repeat 1 (3'-Seq)
- GSM8164240 NIH-3T3 cells, NC AMO treated, repeat 2 (3'-Seq)
- GSM8164241 NIH-3T3 cells, U1 AMO treated, repeat 1 (3'-Seq)
- GSM8164242 NIH-3T3 cells, U1 AMO treated, repeat 2 (3'-Seq)
- GSM8164243 NIH-3T3 cells, U4 AMO treated, repeat 1 (3'-Seq)
- GSM8164244 NIH-3T3 cells, U4 AMO treated, repeat 2 (3'-Seq)
- GSM8164245 HEK-293 cells, NC AMO treated, repeat 1 (3'-Seq)
- GSM8164246 HEK-293 cells, NC AMO treated, repeat 2 (3'-Seq)
- GSM8164247 HEK-293 cells, U1 AMO treated, repeat 1 (3'-Seq)
- GSM8164248 HEK-293 cells, U1 AMO treated, repeat 2 (3'-Seq)
- GSM8164249 HEK-293 cells, U4 AMO treated, repeat 1 (3'-Seq)
- GSM8164250 HEK-293 cells, U4 AMO treated, repeat 2 (3'-Seq)
- GSM8164251 Neuro-2A cells, NC AMO treated, repeat 1 (3'-Seq)
- GSM8164252 Neuro-2A cells, NC AMO treated, repeat 2 (3'-Seq)
- GSM8164253 Neuro-2A cells, U1 AMO treated, repeat 1 (3'-Seq)
- GSM8164254 Neuro-2A cells, U1 AMO treated, repeat 2 (3'-Seq)
- GSM8164255 Neuro-2A cells, U4 AMO treated, repeat 1 (3'-Seq)
- GSM8164256 Neuro-2A cells, U4 AMO treated, repeat 2 (3'-Seq)
- GSM8164257 input DNA, negative control, repeat 1 (ChIP-seq)
- GSM8164258 input DNA, negative control, repeat 2 (ChIP-seq)
- GSM8164259 input DNA, U4 AMO, repeat 1 (ChIP-seq)
- GSM8164260 input DNA, U4 AMO, repeat 2 (ChIP-seq)
- GSM8164261 RNAPII IP, negative control, repeat 1 (ChIP-seq)
- GSM8164262 RNAPII IP, negative control, repeat 2 (ChIP-seq)
- GSM8164263 RNAPII IP, U4 AMO, repeat 1 (ChIP-seq)
- GSM8164264 RNAPII IP, U4 AMO, repeat 2 (ChIP-seq)
- GSM8164265 input DNA, negative control, repeat 3 (ChIP-seq)
- GSM8164266 input DNA, U4 AMO, repeat 3 (ChIP-seq)
+ 2 more — browse all 42 samples with per-sample file links →
- GSE262383 U4 inhibits premature cleavage and polyadenylation of pre-mRNAs [mRNA 3'-seq] 24 samples shares polyadenylation, premature, pre-mrnas, inhibits, cleavage
- GSE250342 Functional inhibition of core spliceosomal machinery activates intronic premature cleavage and polyadenylation of pre-mRNAs 36 samples shares polyadenylation, premature, pre-mrnas, cleavage
- GSE277684 Premature senescence impairs hematopoietic stem cell function during sickle cell disease in mice and humans 52 samples shares premature
- GSE40653 Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs 34 samples shares pre-mrnas
- GSE241209 Tissue factor binds to and inhibits interferon-α receptor-1 signaling 21 samples shares inhibits
- GSE279131 TLDR (True Length of Diverse capped RNAs)-seq: a method for 5’-to-3’ end sequencing of capped full-length RNAs with or without 3’ polyadenylation 18 samples shares polyadenylation
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.