Concomitant loss of TET2 and TET3 results in T cell expansion and genomic instability [BGI-RNA-Seq]
RNA-seq (gene expression) · mouse · 21 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
- 21 samples: 7 × 2nd transplantation B vs 5 × Tet2/3 DKO peripheral CD4 cells B vs 5 × WT_B vs 4 × 1st transplantation BGroups 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
- Concomitant loss of TET2 and TET3 results in T cell expansion and genomic instability in miceCommunications biology · 2024
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 GSE190226_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 PRJNA786484 and SRA study SRP349374. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 21 samples.
How we read this: 4 replicated groups read from 21 sample titles; they account for 21 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.
- GSM5718446 Tet2/3 DKO peripheral CD4 cells BR4 Tet2/3 DKO peripheral C…
- GSM5718447 Tet2/3 DKO peripheral CD4 cells BR5 Tet2/3 DKO peripheral C…
- GSM5718448 2nd transplantation BR1 2nd transplantation B
- GSM5718449 2nd transplantation BR2 2nd transplantation B
- GSM5718450 2nd transplantation BR3 2nd transplantation B
- GSM5718451 2nd transplantation BR4 2nd transplantation B
- GSM5718452 2nd transplantation BR5 2nd transplantation B
- GSM5718453 2nd transplantation BR6 2nd transplantation B
- GSM5718454 2nd transplantation BR7 2nd transplantation B
- GSM5718455 1st transplantation BR4 1st transplantation B
- GSM5718456 WT_BR4 WT_B
- GSM5718457 WT_BR5 WT_B
- GSM5718458 Tet2/3 DKO peripheral CD4 cells BR1 Tet2/3 DKO peripheral C…
- GSM5718459 Tet2/3 DKO peripheral CD4 cells BR2 Tet2/3 DKO peripheral C…
- GSM5718460 Tet2/3 DKO peripheral CD4 cells BR3 Tet2/3 DKO peripheral C…
- GSM5718461 1st transplantation BR1 1st transplantation B
- GSM5718462 1st transplantation BR2 1st transplantation B
- GSM5718463 1st transplantation BR3 1st transplantation B
- GSM5718464 WT_BR1 WT_B
- GSM5718465 WT_BR2 WT_B
- GSM5718466 WT_BR3 WT_B
- GSE278239 Concomitant loss of TET2 and TET3 results in T cell expansion and genomic instability 6 samples shares tet2, tet3, concomitant, instability, expansion, results, loss
- GSE279236 Concomitant loss of TET2 and TET3 results in T cell expansion and genomic instability 31 samples shares tet2, tet3, concomitant, instability, expansion, results, loss
- GSE266580 Ablation of Id1 Reduces Clonal Hematopoiesis, Genomic Instability and Delays Leukemia in Mice with Tet2 Loss of Function [RNA-seq] 12 samples shares tet2, instability, loss
- GSE151211 Tet2 and Tet3 functionally overlap in vitamin C-induced epigenomic alterations in acute myeloid leukemia 49 samples shares tet2, tet3
- GSE190231 Assessing the impact of TET2 and TET3 deletion in TCRa and TCRb expression and repertoire in murine CD4 T cells in physiological and pathological conditions 22 samples shares tet2, tet3
- GSE190229 Assessing the impact of TET2 and TET3 deletion in TCRa and TCRb expression and repertoire in murine CD4 T cells in physiological and pathological conditions [TCR-SEQ] 18 samples shares tet2, tet3
- GSE254998 Loss of TET2 increases B-1 cell number and IgM production while limiting CDR3 diversity 21 samples shares tet2, loss
- GSE27816 Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation 14 samples shares tet2, loss
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.