The transcription factor NFIL3 drives innate lymphoid cell specification from lymphoid progenitors [RNA-seq - Tox]
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 3 × GFP_WT, batch4, vs 3 × GFP_KO, batch4, vs 3 × TOX_WT, batch4, vs 3 × TOX_KO, batch4,Groups 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
- The transcription factor NFIL3 drives innate lymphoid cell specification from lymphoid progenitorsImmunity · 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 GSE291316_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 PRJNA1232811 and SRA study SRP568514. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8833378 GFP_WT, batch4, rep1 GFP_WT, batch4,
- GSM8833379 GFP_WT, batch4, rep2 GFP_WT, batch4,
- GSM8833380 GFP_WT, batch4, rep3 GFP_WT, batch4,
- GSM8833381 GFP_KO, batch4, rep1 GFP_KO, batch4,
- GSM8833382 GFP_KO, batch4, rep2 GFP_KO, batch4,
- GSM8833383 GFP_KO, batch4, rep3 GFP_KO, batch4,
- GSM8833384 TOX_WT, batch4, rep1 TOX_WT, batch4,
- GSM8833385 TOX_WT, batch4, rep2 TOX_WT, batch4,
- GSM8833386 TOX_WT, batch4, rep3 TOX_WT, batch4,
- GSM8833387 TOX_KO, batch4, rep1 TOX_KO, batch4,
- GSM8833388 TOX_KO, batch4, rep2 TOX_KO, batch4,
- GSM8833389 TOX_KO, batch4, rep3 TOX_KO, batch4,
- GSE229129 Conserved transcriptional regulation by BRN1 and BRN2 in neocortical progenitors drives mammalian neural specification and neocortical expansion 13 samples shares transcription, specification, progenitors, drives
- GSE245838 Anchored screening identifies transcription factor blueprints underlying dendritic cell diversity and subset-specific anti-tumor immunity [mouse scRNA-seq] 21 samples shares transcription, rna-seq, factor
- GSE296438 Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at the promoters of genes expressed during meiosis [scRNA-seq & scATAC-seq] 10 samples shares transcription, rna-seq, factor
- GSE286046 Asymmetric Histone Inheritance Regulates Differential Transcription Re-initiation and Cell Fate Decisions in Mouse Olfactory Horizontal Basal Cells 96 samples shares transcription, factor
- GSE282096 Diminished transcriptional activity and splicing changes drive gene length-biased rewiring in the aging transcriptome (RNA-Seq) 94 samples shares transcription, rna-seq
- GSE281037 Large-scale transcriptomic analyses reveal downstream target genes of ZFY1 and ZFY2 transcription factors in male germ cells 48 samples shares transcription, factor
- GSE273878 Cancer-induced FOXP1 disrupts and reprograms skeletal muscle circadian transcription in cachexia [circadian RNA-seq] 48 samples shares transcription, rna-seq
- GSE248585 A conserved epithelial wound-like transcriptional program driven by FOSL1 underlies malignant progression of pancreatic ductal adenocarcinoma (ssRNA-Seq) 46 samples shares transcription, 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.