The transcriptome of WT and DDX55 knockout CD4 naive T cells that activated for indicated time points
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: 12 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.
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 GSE263251_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 PRJNA1096351 and SRA study SRP499839. 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 12 sample titles: 12 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.
- GSM8188605 WT_CD4_naive T_0h_RNA_1
- GSM8188606 WT_CD4_ naive T_0h_RNA_2
- GSM8188607 WT_CD4_naive T_8h_RNA_1
- GSM8188608 WT_CD4_ naive T_8h_RNA_2
- GSM8188609 WT_CD4_naive T_24h_RNA_1
- GSM8188610 WT_CD4_ naive T_24h_RNA_2
- GSM8188611 DDX55_KO_CD4_naive T_0h_RNA_1
- GSM8188612 DDX55_KO_CD4_ naive T_0h_RNA_2
- GSM8188613 DDX55_KO_CD4_naive T_8h_RNA_1
- GSM8188614 DDX55_KO_CD4_ naive T_8h_RNA_2
- GSM8188615 DDX55_KO_CD4_naive T_24h_RNA_1
- GSM8188616 DDX55_KO_CD4_ naive T_24h_RNA_2
- GSE280858 Gene expression profile at single cell level of OVA+ cells elicited by LTA1/OVA vaccine at different time points and CD4+T cells from naïve spleen as control 10 samples shares cd4, points, time
- GSE278003 Single cell RNA sequencing of CD45+ immune cells from tumor and tumor-adjacent mammary adipose tissue in a postmenopausal breast cancer model of lean, obese, and weight loss Trem2+/+ and Trem2-/- mice 92 samples shares cd4
- GSE235059 ICOSL, OX40L, and CD30L Control Persistence of Asthmatic CD4 Trm Cells 80 samples shares cd4
- GSE201228 CD4+ T cell activation in absence of WNK1 72 samples shares cd4
- GSE222996 The immune landscape of the “deregulated host response” in sepsis: newly emerging MDSCs with high expression of CD47 leads to B cell suppression via App-CD74 signaling [RNA-seq] 61 samples shares cd4
- GSE197425 TGF-β specifies TFH versus TH17 cell fates in murine CD4+ T cells through c-Maf (Seq03, bulk-RNAseq) 34 samples shares cd4
- GSE248155 Effect of regorafenib, anti-PD1, and anti-CD40 agonist in Head and Neck Squamous Cell Carcinoma 31 samples shares cd4
- GSE325195 Dendritic cell redundancy enables priming of anti-tumor CD4 T cells in pancreatic cancer 30 samples shares cd4
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.