Epigenetic and transcriptional alterations in Kmt2c/Kmt2d-deficient gastric cancer [RNA-seq]
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 6 conditions, mostly in duplicateGroups 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 GSE316994_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 PRJNA1405649 and SRA study SRP664782. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9463543 TPCD_DMSO_Rep1 TPCD_DMSO
- GSM9463544 TPCD_DMSO_Rep2 TPCD_DMSO
- GSM9463545 TPCD_Rapa_Rep1 TPCD_Rapa
- GSM9463546 TPCD_Rapa_Rep2 TPCD_Rapa
- GSM9463547 TP_DMSO_Rep1 TP_DMSO
- GSM9463548 TP_DMSO_Rep2 TP_DMSO
- GSM9463549 TP_Rapa_Rep1 TP_Rapa
- GSM9463550 TP_Rapa_Rep2 TP_Rapa
- GSM9463551 TY_DMSO_Rep1 TY_DMSO
- GSM9463552 TY_DMSO_Rep2 TY_DMSO
- GSM9463553 TY_Rapa_Rep1 TY_Rapa
- GSM9463554 TY_Rapa_Rep2 TY_Rapa
- GSE335970 KMT2C catalytic activity regulates enhancer H3K4me1 and synaptic gene expression in cortical excitatory neurons [RNA-Seq] 39 samples shares kmt2c, rna-seq
- GSE300014 The CARM1 Epigenetic Enzyme Inhibits Cross-presenting Dendritic Cell Function in Cancer Immunity [RNA-seq] 26 samples shares epigenetic, rna-seq
- GSE241770 ACSS2 mediates an epigenetic pathway to regulate maternal Beta-cell adaptation and progression of gestational diabetes (scRNA-Seq) 7899 samples shares epigenetic, rna-seq
- GSE309564 IFNg shapes macrophage inflammatory responses by STAT1 isoform-specific epigenetic and transcriptional mechanisms [RNA-Seq] 72 samples shares epigenetic, rna-seq
- GSE243942 Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [RNA-seq] 125 samples shares epigenetic, rna-seq
- GSE276155 RBBP5 is an epigenetic regulator of mammalian hepatic 12h oscillator [RNA-seq] 96 samples shares epigenetic, rna-seq
- GSE289641 Noncanonical PRC2 chromatin association reveals a key role of EZHIP in intergenerational epigenetic memory transition [RNA-Seq] 68 samples shares epigenetic, rna-seq
- GSE247454 Brca1 haploinsufficiency promotes early tumor onset and epigenetic alterations in a mouse model of hereditary breast cancer 38 samples shares alterations, epigenetic
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.