SMARCB1 loss defines a novel PTCL-NOS subtype displaying an immunosuppressive TME susceptible to HDAC inhibitors
RNA-seq (gene expression) · mouse · 13 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
- 13 samples: 11 distinct titles, 2 of them repeatedGroups 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
- Lack of SMARCB1 expression characterizes a subset of human and murine peripheral T-cell lymphomasNature communications · 2024
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 GSE190276_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 PRJNA786571 and SRA study SRP349419. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 13 sample titles: 11 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.
- GSM5718990 04__T15smarcb1A1
- GSM5718991 05__T15smarcb1A2
- GSM5718992 06__T15smarcb1A3
- GSM5718993 07__ctrl_n1
- GSM5718994 08__ctrl_n2
- GSM5718995 09__ctrl_n3
- GSM5718996 13__SAHA_n1
- GSM5718997 14__SAHA_n2
- GSM5718998 15__SAHA_n3
- GSM5718999 CD4Smarcb1_9
- GSM5719000 CD4Smarcb1_20
- GSM5719001 PTCL_SAHA_49
- GSM5719002 PTCL_SAHA_54
- GSE273148 TGF-β builds a dual immune barrier in colorectal cancer by impairing T cell recruitment and instructing immunosuppressive SPP1+ macrophages 23 samples shares tme, immunosuppressive
- GSE249630 Modeling T cell temporal response to cancer immunotherapy rationalize development of combinatorial treatments protocols 1372 samples shares tme
- GSE332646 Bulk RNA-seq of juvenile mouse liver following NDMA or saline treatment in WT and Mgmt-/- genotypes across multiple timepoints 214 samples shares tme
- GSE298006 Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [RNA-Seq] 110 samples shares tme
- 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 tme
- GSE276784 Inflammation perturbs hematopoiesis by remodeling specific compartments of the bone marrow niche 89 samples shares tme
- GSE235623 MERTK inhibition for the treatment of tissue fibrosis [RNA-seq] 86 samples shares tme
- GSE261670 ASOs are an effective treatment for disease-associated oligodendrocyte signatures in premanifest and symptomatic SCA3 mice 74 samples shares tme
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.