Optimized reporters for multiplexed detection of transcription factor activity
RNA-seq (gene expression) · human · 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
- Homo sapiens (human)
- Samples
- 14 samples: 6 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.
- Paper
- Optimized reporters for multiplexed detection of transcription factor activitybioRxiv : the preprint server for biology · 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 GSE267969_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 PRJNA1112759 and SRA study SRP508325. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 6 replicated groups read from 14 sample titles; they account for 14 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.
- GSM8282641 mNPCs derived from mES-E14TG2a, biological replicate 1 mNPCs derived from mES-…
- GSM8282642 mNPCs derived from mES-E14TG2a, biological replicate 2 mNPCs derived from mES-…
- GSM8552373 mES-E14TG2a, biological replicate 1 mES-E14TG2a,
- GSM8552374 mES-E14TG2a, biological replicate 2 mES-E14TG2a,
- GSM8552375 mES-E14TG2a, biological replicate 3 mES-E14TG2a,
- GSM8552376 HepG2, biological replicate 1 HepG2,
- GSM8552377 HepG2, biological replicate 2 HepG2,
- GSM8552378 HepG2, biological replicate 3 HepG2,
- GSM8552379 HepG2 MTF1 KD, biological replicate 1 HepG2 MTF1 KD,
- GSM8552380 HepG2 MTF1 KD, biological replicate 2 HepG2 MTF1 KD,
- GSM8552381 HepG2 NRF1 KD, biological replicate 1 HepG2 NRF1 KD,
- GSM8552382 HepG2 NRF1 KD, biological replicate 2 HepG2 NRF1 KD,
- GSM8552383 HepG2 HNF1A KD, biological replicate 1 HepG2 HNF1A KD,
- GSM8552384 HepG2 HNF1A KD, biological replicate 2 HepG2 HNF1A KD,
- GSE239704 NF-κB transcription factors RelA and c-Rel selectively control CD4+ T-cell function in multiple sclerosis and cancer 34 samples shares transcription, factor
- GSE256246 Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function. 132 samples shares transcription, factor
- GSE286473 FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry 95 samples shares transcription, factor
- GSE251674 Redistribution of PU.1 partner transcription factor RUNX1 binding secures cell survival during leukemogenesis 79 samples shares transcription, factor
- GSE43916 Hierarchical mechanisms for transcription factor-mediated reprogramming of fibroblasts to neurons 38 samples shares transcription, factor
- GSE218862 ZBTB24 is a conserved multifaceted transcription factor at genes and centromeres that governs the DNA methylation state and expression of satellite repeats [ChIP-Seq] 20 samples shares transcription, factor
- GSE267455 IRF2BP2 affects T-ALL cell proliferation by cooperating with master transcription factors 19 samples shares transcription, factor
- GSE225993 Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [ATAC-seq] 16 samples shares transcription, factor
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.