CCCTC-binding Factor N-terminal Domain Regulates Clustered Protocadherin Gene Expression by Enhancing Cohesin Processivity [RNA-Seq]
RNA-seq (gene expression) · mouse · 47 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 47 samples: 47 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
- CCCTC-binding factor N-terminal domain regulates clustered protocadherin gene expression by enhancing cohesin processivityThe Journal of biological chemistry · 2025
Read the full summary ↓
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 GSE285577_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1204915 and SRA study SRP554645. 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 47 sample titles: 47 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.
- GSM8705103 P0_cortex, WT, rep1, RNA-seq
- GSM8705104 P0_cortex, WT, rep2, RNA-seq
- GSM8705105 P0_cortex, WT, rep3, RNA-seq
- GSM8705106 P0_cortex, WT, rep4, RNA-seq
- GSM8705107 P0_cortex, HET, rep1, RNA-seq
- GSM8705108 P0_cortex, HET, rep2, RNA-seq
- GSM8705109 P0_cortex, HET, rep3, RNA-seq
- GSM8705110 P0_cortex, HET, rep4, RNA-seq
- GSM8705111 Adult_cortex, WT, rep1, RNA-seq
- GSM8705112 Adult_cortex, WT, rep2, RNA-seq
- GSM8705113 Adult_cortex, WT, rep3, RNA-seq
- GSM8705114 Adult_cortex, HET, rep1, RNA-seq
- GSM8705115 Adult_cortex, HET, rep2, RNA-seq
- GSM8705116 Adult_cortex, HET, rep3, RNA-seq
- GSM8705117 Adult_ob, WT, rep1, RNA-seq
- GSM8705118 Adult_ob, WT, rep2, RNA-seq
- GSM8705119 Adult_ob, WT, rep3, RNA-seq
- GSM8705120 Adult_ob, HET, rep1, RNA-seq
- GSM8705121 Adult_ob, HET, rep2, RNA-seq
- GSM8705122 Adult_ob, HET, rep3, RNA-seq
- GSM8705123 N2A, WT, rep1, RNA-seq
- GSM8705124 N2A, WT, rep2, RNA-seq
- GSM8705125 N2A, WT, rep3, RNA-seq
- GSM8705126 N2A, ADA-Clone1, rep1, RNA-seq
- GSM8705127 N2A, ADA-Clone1, rep2, RNA-seq
- GSM8705128 N2A, ADA-Clone1, rep3, RNA-seq
- GSM8705129 N2A, ADA-Clone2, rep1, RNA-seq
- GSM8705130 N2A, ADA-Clone2, rep2, RNA-seq
- GSM8705131 N2A, ADA-Clone2, rep3, RNA-seq
- GSM8753167 N2A, shCtr, rep1, RNA-seq
- GSM8753168 N2A, shCtr, rep2, RNA-seq
- GSM8753169 N2A, shCtr, rep3, RNA-seq
- GSM8753170 N2A, shWAPL-1, rep1, RNA-seq
- GSM8753171 N2A, shWAPL-1, rep2, RNA-seq
- GSM8753172 N2A, shWAPL-1, rep3, RNA-seq
- GSM8753173 N2A, shWAPL-2, rep1, RNA-seq
- GSM8753174 N2A, shWAPL-2, rep2, RNA-seq
- GSM8753175 N2A, shWAPL-2, rep3, RNA-seq
- GSM8753176 N2A, shWAPL-3, rep1, RNA-seq
- GSM8753177 N2A, shWAPL-3, rep2, RNA-seq
+ 7 more — browse all 47 samples with per-sample file links →
- GSE285578 CTCF N-terminal Domain Regulates Clustered Protocadherin Gene Expression by Enhancing Cohesin Processivity [ChIP-seq] 20 samples shares protocadherin, processivity, n-terminal, clustered, enhancing, cohesin
- GSE249430 Cohesin trajectories shape the epigenetic and transcriptional landscape of clustered Protocadherin genes for single neuron identities 80 samples shares protocadherin, clustered, cohesin
- GSE239632 Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation [RNA-Seq] 15 samples shares n-terminal, rna-seq
- GSE239637 Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation [scRNA-Seq] 4 samples shares n-terminal, rna-seq
- GSE310953 A new mouse mutant with a discrete mutation in Pcdhgc5 reveals that the Protocadherin gC5 isoform is not essential for dendrite arborization in the cerebral cortex 12 samples shares protocadherin
- GSE252989 The N-terminal domain of gasdermin D induces liver fibrosis by reprogrammed lipid metabolism 9 samples shares n-terminal
- GSE229603 Protocadherin 8 and transcription factor Dbx1 regulate the formation of developing cerebral cortex 2 samples shares protocadherin
- GSE239638 Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation 79 samples shares n-terminal
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.