HIV-1 reprograms CD4 T cell responses by impairing antigen-specific communication with dendritic cells
RNA-seq (gene expression) · mouse · 8 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
- 8 samples: 8 × OT-II.2 CD4 T cell-BMDC co-culture_sublibGroups 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.
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 GSE304995_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 PRJNA1303660 and SRA study SRP607663. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 1 replicated groups read from 8 sample titles; they account for 8 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.
- GSM9160751 OT-II.2 CD4 T cell-BMDC co-culture_sublib1 OT-II.2 CD4 T cell-BMDC…
- GSM9160752 OT-II.2 CD4 T cell-BMDC co-culture_sublib2 OT-II.2 CD4 T cell-BMDC…
- GSM9160753 OT-II.2 CD4 T cell-BMDC co-culture_sublib3 OT-II.2 CD4 T cell-BMDC…
- GSM9160754 OT-II.2 CD4 T cell-BMDC co-culture_sublib4 OT-II.2 CD4 T cell-BMDC…
- GSM9160755 OT-II.2 CD4 T cell-BMDC co-culture_sublib5 OT-II.2 CD4 T cell-BMDC…
- GSM9160756 OT-II.2 CD4 T cell-BMDC co-culture_sublib6 OT-II.2 CD4 T cell-BMDC…
- GSM9160757 OT-II.2 CD4 T cell-BMDC co-culture_sublib7 OT-II.2 CD4 T cell-BMDC…
- GSM9160758 OT-II.2 CD4 T cell-BMDC co-culture_sublib8 OT-II.2 CD4 T cell-BMDC…
- GSE275471 Proximity-dependent labeling identifies dendritic cells that prime the antitumor CD4+ T cell response 857 samples shares cd4, dendritic
- GSE325195 Dendritic cell redundancy enables priming of anti-tumor CD4 T cells in pancreatic cancer 30 samples shares cd4, dendritic
- GSE260791 Correction of age-associated defects in dendritic cell functions enables CD4+T cells to eradicate tumors in the elderly 30 samples shares cd4, dendritic
- GSE283198 Combined Flt3L and CD40 agonism restores dendritic cell driven T cell immunity in mouse models and patients with pancreatic cancer [mouse] 13 samples shares cd4, dendritic
- 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
- GSE227937 MicroRNA-150 controls experimental autoimmune encephalomyelitis by regulating CD4 T cell differentiation and function 69 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.