Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (RNA-Seq)
RNA-seq (gene expression) · mouse · 26 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
- 26 samples: 13 conditions, mostly in duplicateGroups 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 GSE261222_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 PRJNA1083571 and SRA study SRP493257. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 26 samples.
How we read this: 13 replicated groups read from 26 sample titles; they account for 26 of them. 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.
- GSM8138053 RNA-seq of wt mouse ESC_R1 RNA-seq of wt mouse ESC
- GSM8138054 RNA-seq of wt mouse ESC_R2 RNA-seq of wt mouse ESC
- GSM8138055 RNA-seq of Zfp608 promoter deletion in mouse ESC_R1 RNA-seq of Zfp608 promo…
- GSM8138056 RNA-seq of Zfp608 promoter deletion in mouse ESC_R2 RNA-seq of Zfp608 promo…
- GSM8138057 RNA-seq of polyA insertion at Zfp608 in mouse ESC_R1 RNA-seq of polyA insert…
- GSM8138058 RNA-seq of polyA insertion at Zfp608 in mouse ESC_R2 RNA-seq of polyA insert…
- GSM8138059 RNA-seq of element A deletion in mouse ESC_R1 RNA-seq of element A de…
- GSM8138060 RNA-seq of element A deletion in mouse ESC_R2 RNA-seq of element A de…
- GSM8138061 RNA-seq of element B deletion in mouse ESC_R1 RNA-seq of element B de…
- GSM8138062 RNA-seq of element B deletion in mouse ESC_R2 RNA-seq of element B de…
- GSM8138063 RNA-seq of element A and B deletion in mouse ESC_R1 RNA-seq of element A an…
- GSM8138064 RNA-seq of element A and B deletion in mouse ESC_R2 RNA-seq of element A an…
- GSM8138065 RNA-seq of Pax6 upregulation in mouse ESC_R1 RNA-seq of Pax6 upregul…
- GSM8138066 RNA-seq of Pax6 upregulation in mouse ESC_R2 RNA-seq of Pax6 upregul…
- GSM8138067 RNA-seq of wt mouse NPC_R1 RNA-seq of wt mouse NPC
- GSM8138068 RNA-seq of wt mouse NPC_R2 RNA-seq of wt mouse NPC
- GSM8138069 RNA-seq of Zfp608 promoter deletion in mouse NPC_R1 RNA-seq of Zfp608 promo…
- GSM8138070 RNA-seq of Zfp608 promoter deletion in mouse NPC_R2 RNA-seq of Zfp608 promo…
- GSM8138071 RNA-seq of polyA insertion at Zfp608 in mouse NPC_R1 RNA-seq of polyA insert…
- GSM8138072 RNA-seq of polyA insertion at Zfp608 in mouse NPC_R2 RNA-seq of polyA insert…
- GSM8138073 RNA-seq of element A deletion in mouse NPC_R1 RNA-seq of element A de…
- GSM8138074 RNA-seq of element A deletion in mouse NPC_R2 RNA-seq of element A de…
- GSM8138075 RNA-seq of element B deletion in mouse NPC_R1 RNA-seq of element B de…
- GSM8138076 RNA-seq of element B deletion in mouse NPC_R2 RNA-seq of element B de…
- GSM8138077 RNA-seq of element A and B deletion in mouse NPC_R1 RNA-seq of element A an…
- GSM8138078 RNA-seq of element A and B deletion in mouse NPC_R2 RNA-seq of element A an…
- GSE261221 Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (ChIP-Seq) 189 samples shares zfp608, architecture, scaffolding, element, rewires, locus
- GSE308227 Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus [ATAC-Seq and Hi-C] 10 samples shares zfp608, architecture, scaffolding, element, rewires, locus
- GSE262551 A Scaffolding Element Rewires Local 3D Chromatin Architecture During Differentiation 255 samples shares architecture, scaffolding, element, rewires
- GSE275499 TEX cell fate and differentiation are shaped by 3D genome reorganization and chromatin architecture integrity [RNA-seq] 18 samples shares architecture, rna-seq
- GSE295250 Conserved Noncoding Cis-Elements Associated with Hibernation Modulate Metabolic and Behavioral Adaptations in Mice [RNA-seq] 72 samples shares element, rna-seq
- GSE288110 TBP regulates transposable element expression in early mouse embryos [RNA-seq] 49 samples shares element, rna-seq
- GSE266176 Tranposable Element Control by TRIM28 Safeguards PGC Sex Determination Program [RNA-Seq] 42 samples shares element, rna-seq
- GSE206159 Stepwise de novo establishment of inactive X chromosome architecture in early development [Embryo RNA-seq] 42 samples shares architecture, rna-seq
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.