Investigating Immune Escape of Chronic Myeloid Leukemia in Blast Crisis by Comparing T cells from miR-142 KO BCR-ABL versus miR-142 WT BCR-ABL mice
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 × CP CML T cells vs 6 × BC CML T cellsGroups 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 GSE261822_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 PRJNA1089161 and SRA study SRP486081. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 2 replicated groups read from 24 sample titles; they account for 14 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.
- GSM8037205 scRNA-seq of WT-LMPP
- GSM8037206 scRNA-seq of KO-LMPP
- GSM8037207 scRNA-seq of WT-CML-LMPP
- GSM8037208 scRNA-seq of KO-CML-LMPP
- GSM8037209 scRNA-seq of WT-CML-PBMC
- GSM8037210 scRNA-seq of WT-CML-BM cells
- GSM8037211 scRNA-seq of WT-CML-SPLEEN-T cells
- GSM8037212 scRNA-seq of KO-CML-PBMC
- GSM8037213 scRNA-seq of KO-CML-BM cells
- GSM8037214 scRNA-seq of KO-CML-SPLEEN-T cells
- GSM8152164 CP CML T cells 1 CP CML T cells
- GSM8152165 CP CML T cells 2 CP CML T cells
- GSM8152166 CP CML T cells 3 CP CML T cells
- GSM8152167 CP CML T cells 4 CP CML T cells
- GSM8152168 CP CML T cells 5 CP CML T cells
- GSM8152169 CP CML T cells 6 CP CML T cells
- GSM8152170 CP CML T cells 7 CP CML T cells
- GSM8152171 CP CML T cells 8 CP CML T cells
- GSM8152172 BC CML T cells 1 BC CML T cells
- GSM8152173 BC CML T cells 2 BC CML T cells
- GSM8152174 BC CML T cells 3 BC CML T cells
- GSM8152175 BC CML T cells 4 BC CML T cells
- GSM8152176 BC CML T cells 5 BC CML T cells
- GSM8152177 BC CML T cells 6 BC CML T cells
- GSE266394 Gene expression profiling of murine BCR-ABL(p185)-positive CDK6-WT, CDK6-K43M and CDK6-KO cells 3 samples shares bcr-abl
- GSE264219 ChIP seq of CDK6-WT and CDK6-K43M in murine BCR-ABL(p185)+ pre/pro B-cells 6 samples shares bcr-abl
- GSE57543 Expression data from B6 mouse miR-142 KO and WT T cells 6 samples shares mir-142
- GSE266393 ATAC seq in murine BCR-ABL(p185)-positive pre/pro B-cells expressing wildtype CDK6 or a kinase-dead mutant (CDK6 K43M) 3 samples shares bcr-abl
- GSE233544 Investigating T cell responses in the dura to systemic infection 58 samples shares investigating
- GSE227267 Investigating ovarian disrupting effects of per- and polyfluoroalkyl substances 44 samples shares investigating
- GSE337368 Investigating the effects of IFN-gamma on attached and detached ovarian cancer cells 24 samples shares investigating
- GSE275887 Investigating the potential molecular mechanisms of mogroside V on glucose homeostasis by transcriptome profiling of adult mouse hypothalamic cells 24 samples shares investigating
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.