Loss of tumor cell MHC Class II drives MAPK-inhibitor insensitivity of BRAF-mutant anaplastic thyroid cancers [RNA-seq]
RNA-seq (gene expression) · mouse · 24 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
- 24 samples: 8 conditions, mostly in triplicateGroups 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
- Loss of tumor cell MHC class II drives MAPK inhibitor insensitivity of BRAF-mutant anaplastic thyroid cancersThe Journal of clinical investigation · 2025
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 GSE302629_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 PRJNA1291621 and SRA study SRP601127. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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.
- GSM9107705 RNA_Prim_B92_IFNG_rep1 RNA_Prim_B92_IFNG
- GSM9107706 RNA_Prim_B92_IFNG_rep2 RNA_Prim_B92_IFNG
- GSM9107707 RNA_Prim_B92_IFNG_rep3 RNA_Prim_B92_IFNG
- GSM9107708 RNA_Prim_B92_IFNGandTram_rep1 RNA_Prim_B92_IFNGandTram
- GSM9107709 RNA_Prim_B92_IFNGandTram_rep2 RNA_Prim_B92_IFNGandTram
- GSM9107710 RNA_Prim_B92_IFNGandTram_rep3 RNA_Prim_B92_IFNGandTram
- GSM9107711 RNA_Prim_B92_Tram_rep1 RNA_Prim_B92_Tram
- GSM9107712 RNA_Prim_B92_Tram_rep2 RNA_Prim_B92_Tram
- GSM9107713 RNA_Prim_B92_Tram_rep3 RNA_Prim_B92_Tram
- GSM9107714 RNA_Prim_B92_Vehicle_rep1 RNA_Prim_B92_Vehicle
- GSM9107715 RNA_Prim_B92_Vehicle_rep2 RNA_Prim_B92_Vehicle
- GSM9107716 RNA_Prim_B92_Vehicle_rep3 RNA_Prim_B92_Vehicle
- GSM9107717 RNA_Rec_B36934_IFNG_rep1 RNA_Rec_B36934_IFNG
- GSM9107718 RNA_Rec_B36934_IFNG_rep2 RNA_Rec_B36934_IFNG
- GSM9107719 RNA_Rec_B36934_IFNG_rep3 RNA_Rec_B36934_IFNG
- GSM9107720 RNA_Rec_B36934_IFNGandTram_rep1 RNA_Rec_B36934_IFNGandT…
- GSM9107721 RNA_Rec_B36934_IFNGandTram_rep2 RNA_Rec_B36934_IFNGandT…
- GSM9107722 RNA_Rec_B36934_IFNGandTram_rep3 RNA_Rec_B36934_IFNGandT…
- GSM9107723 RNA_Rec_B36934_Tram_rep1 RNA_Rec_B36934_Tram
- GSM9107724 RNA_Rec_B36934_Tram_rep2 RNA_Rec_B36934_Tram
- GSM9107725 RNA_Rec_B36934_Tram_rep3 RNA_Rec_B36934_Tram
- GSM9107726 RNA_Rec_B36934_Vehicle_rep1 RNA_Rec_B36934_Vehicle
- GSM9107727 RNA_Rec_B36934_Vehicle_rep2 RNA_Rec_B36934_Vehicle
- GSM9107728 RNA_Rec_B36934_Vehicle_rep3 RNA_Rec_B36934_Vehicle
- GSE302631 Loss of tumor cell MHC Class II drives MAPK-inhibitor insensitivity of BRAF-mutant anaplastic thyroid cancers 40 samples shares mhc, mapk-inhibitor, insensitivity, braf-mutant, anaplastic, thyroid, drives
- GSE302630 Loss of tumor cell MHC Class II drives MAPK-inhibitor insensitivity of BRAF-mutant anaplastic thyroid cancers [ATAC-seq] 16 samples shares mhc, mapk-inhibitor, insensitivity, braf-mutant, anaplastic, thyroid, drives
- GSE293728 IFN-γ-STAT1 Axis Drives MHC-II Antigen Presentation Potentiation in Tumor Associated Macrophages 18 samples shares mhc, drives
- GSE129746 RNA-seq data of Ly6Chigh CD11c+ MHC-II+ and Ly6C low cells FACS-sorted from Mock-LLC and SULT2B1b-LLC tumors 15 samples shares mhc, rna-seq
- GSE284168 Mammalian queuosine tRNA modification impacts codon usage preferences to enhance cell proliferation and MHC-II expression [BMDC_0v100Q_mRNA-seq] 6 samples shares mhc, rna-seq
- GSE272880 Cytoplasmic UHRF1 restrains MHC-I-mediated anti-tumor immune response [bulk RNA-seq] 6 samples shares mhc, rna-seq
- GSE330011 Regulatory T cells Restrain CD4 T Cell Control of MHC-I-Deficient Metastatic Pancreatic Cancer Emerging After PD-L1 Blockade [scRNA-seq] 2 samples shares mhc, rna-seq
- GSE307658 scRNA-seq of MHCII-KO and WT B cells during influenza infection 4 samples shares mhc, rna-seq
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.