An Unbiased Approach to Identifying Cellular Reprogramming-Inducible Enhancers [RNA-seq]
RNA-seq (gene expression) · mouse · 14 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
- 14 samples: 14 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
- An Unbiased Approach to Identifying Cellular Reprogramming-Inducible EnhancersInternational journal of molecular sciences · 2024
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 GSE274132_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 PRJNA1145011 and SRA study SRP524552. 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 14 sample titles: 14 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.
- GSM8443993 MEFs (Day 0), biol rep 1, RNA-seq
- GSM8443994 MEFs (Day 0), biol rep 2, RNA-seq
- GSM8443995 MEFs treated with doxycycline, Day 1, biol rep 1, RNA-seq
- GSM8443996 MEFs treated with doxycycline, Day 1, biol rep 2, RNA-seq
- GSM8443997 MEFs treated with doxycycline, Day 2, biol rep 1, RNA-seq
- GSM8443998 MEFs treated with doxycycline, Day 2, biol rep 2, RNA-seq
- GSM8443999 MEFs treated with doxycycline, Day 3, biol rep 1, RNA-seq
- GSM8444000 MEFs treated with doxycycline, Day 3, biol rep 2, RNA-seq
- GSM8444001 MEFs treated with doxycycline, Day 4, biol rep 1, RNA-seq
- GSM8444002 MEFs treated with doxycycline, Day 4, biol rep 2, RNA-seq
- GSM8444003 MEFs treated with doxycycline, Day 6, biol rep 1, RNA-seq
- GSM8444004 MEFs treated with doxycycline, Day 6, biol rep 2, RNA-seq
- GSM8444005 MEFs treated with doxycycline, Day 8, biol rep 1, RNA-seq
- GSM8444006 MEFs treated with doxycycline, Day 8, biol rep 2, RNA-seq
- GSE219229 Unbiased profiling of clinical kinase inhibitors’ effects in activated macrophages using chromatin modifications as high-content readouts [RNA-Seq] 180 samples shares unbiased, rna-seq
- GSE339044 Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain [RNA-Seq] 71 samples shares enhancers, rna-seq
- GSE294336 BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis [RNA-seq Aged_adult] 48 samples shares enhancers, rna-seq
- GSE294339 BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis [RNA-seq Col14] 48 samples shares enhancers, rna-seq
- GSE218968 Unbiased profiling of clinical kinase inhibitors’ effects in activated macrophages using chromatin modifications as high-content readouts [Chromatin associated RNA-seq] 27 samples shares unbiased, rna-seq
- GSE276734 3D Chromatin organization of signal-induced specific enhancers safeguards early ESC differentiation by promoting cluster gene expression [RNA-seq] 21 samples shares enhancers, rna-seq
- GSE271862 The Sotos syndrome gene Nsd1 safeguards bivalent developmental enhancers in poised states through restraining excessive H3K27me3 deposition [RNA-Seq] 18 samples shares enhancers, rna-seq
- GSE275105 Mutant-p53 stimulates Cxcl1 Expression from Distal Enhancers to Suppress Immune Response to Pancreatic Cancer [RNA-seq] 13 samples shares enhancers, 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.