Transcriptome Profile of IEC4.1 cells deficient with Prdm1 in response to IFN-gamma
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 × IEC4.1 WT Ctrl vs 3 × IEC4.1 WT + IFNγ vs 3 × IEC4.1 PRDM1 KO ctrl vs 3 × IEC4.1 PRDM1 KO +IFNγGroups 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
- Targeting the interaction between long noncoding RNA XR_001779380 and Prdm1 to enhance IFN-γ immunity in murine neonatal intestinal epithelial cellsmBio · 2025
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 GSE245345_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 PRJNA1027862 and SRA study SRP466280. 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.
- GSM7841124 IEC4.1 WT Ctrl 1 IEC4.1 WT Ctrl
- GSM7841125 IEC4.1 WT Ctrl 2 IEC4.1 WT Ctrl
- GSM7841126 IEC4.1 WT Ctrl 3 IEC4.1 WT Ctrl
- GSM7841127 IEC4.1 WT + IFNγ 1 IEC4.1 WT + IFNγ
- GSM7841128 IEC4.1 WT + IFNγ 2 IEC4.1 WT + IFNγ
- GSM7841129 IEC4.1 WT + IFNγ 3 IEC4.1 WT + IFNγ
- GSM7841130 IEC4.1 PRDM1 KO ctrl 1 IEC4.1 PRDM1 KO ctrl
- GSM7841131 IEC4.1 PRDM1 KO ctrl 2 IEC4.1 PRDM1 KO ctrl
- GSM7841132 IEC4.1 PRDM1 KO ctrl 3 IEC4.1 PRDM1 KO ctrl
- GSM7841133 IEC4.1 PRDM1 KO +IFNγ 1 IEC4.1 PRDM1 KO +IFNγ
- GSM7841134 IEC4.1 PRDM1 KO +IFNγ 2 IEC4.1 PRDM1 KO +IFNγ
- GSM7841135 IEC4.1 PRDM1 KO +IFNγ 3 IEC4.1 PRDM1 KO +IFNγ
- GSE245533 Next Generation Sequencing Analysis of Transcriptome Profile in CRISPR/Cas9 U90926KO IEC4.1 Cells Treated with IFN-gamma protein (IFNγ) 12 samples shares iec4, ifn-gamma
- GSE245478 Transcriptomic profile of IEC4.1 cells treated with an ASO to lncRNA XR_001779380 in response to IFN-gamma 12 samples shares iec4, ifn-gamma
- GSE294881 RNA sequencing of Tcf7 and Prdm1 deficient T cells [RNAseq_Tcf7Prdm1DKO] 8 samples shares prdm1, deficient
- GSE242882 CPEB2-activated Prdm16 translation promotes brown adipocyte function and prevents obesity 22 samples shares prdm1
- GSE309484 Lineage-specific enhancer insertions regulate Prdm14 to drive the rapid transition from naïve to formative pluripotency in rodents 16 samples shares prdm1
- GSE305275 PRDM16 controls smooth muscle cell fate in atherosclerosis [RNA-Seq] 16 samples shares prdm1
- GSE297494 Total RNA transcriptomic profiling of mouse thoracic and abdominal perivascular adipose tissue of mice with an adipocyte-specific deletion of PRDM16 and flox control mice. 15 samples shares prdm1
- GSE271196 Prdm16os is a brain and astrocyte-specific lncRNA implicated with Alzheimer’s disease 12 samples shares prdm1
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.