Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size (RNA-seq NPC)
RNA-seq (gene expression) · mouse · 18 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
- 18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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
- Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain sizeNeuron · 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 GSE220459_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 PRJNA909807 and SRA study SRP411876. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 18 sample titles: 18 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.
- GSM6805152 Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#3, 72 hours [UC_3]
- GSM6805153 Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#4, 72 hours [UC_4]
- GSM6805154 Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#5, 72 hours [UC_5]
- GSM6805155 Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#6, 72 hours [UC_6]
- GSM6805156 Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#8, 72 hours [UC_8]
- GSM6805157 Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#9, 72 hours [UC_9]
- GSM6805158 Upf2fl/fl NPCs, No treatment biol rep#3, 72 hours [UM_3]
- GSM6805159 Upf2fl/fl NPCs, No treatment biol rep#4, 72 hours [UM_4]
- GSM6805160 Upf2fl/fl NPCs, No treatment biol rep#5, 72 hours [UM_5]
- GSM6805161 Upf2fl/fl NPCs, No treatment biol rep#6, 72 hours [UM_6]
- GSM6805162 Upf2fl/fl NPCs, No treatment biol rep#8, 72 hours [UM_8]
- GSM6805163 Upf2fl/fl NPCs, No treatment biol rep#9, 72 hours [UM_9]
- GSM6805164 Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#3, 72 hours [UP_C3]
- GSM6805165 Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#4, 72 hours [UP_C4]
- GSM6805166 Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#5, 72 hours [UP_C5]
- GSM6805167 Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#6, 72 hours [UP_C6]
- GSM6805168 Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#8, 72 hours [UP_C8]
- GSM6805169 Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#9, 72 hours [UP_C9]
- GSE220462 Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size 34 samples shares trp53, nmd, interactions, maintenance, progenitor, epistatic, control
- GSE301965 Type I IFN impedes early bacterial control in TB-resistant and -susceptible mice and activates neutrophils to restrict lung macrophage-T cell interactions 72 samples shares interactions, control
- GSE298786 Type I IFN impedes early bacterial control in TB-resistant and -susceptible mice and activates neutrophils to restrict lung macrophage-T cell interactions [RNA-seq] 70 samples shares interactions, control
- GSE267441 Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [RNA-seq] 35 samples shares interactions, epistatic
- GSE302734 Single-Cell RNA Sequencing Unravels Interactions between Macrophages and Fibroadipogenic Progenitors during Ectopic Bone Formation in FOP Mice 12 samples shares interactions, progenitor
- GSE316171 Fibroblast Growth Factor Receptor Signaling in Maturing Osteoblasts Controls Cell-Matrix Interactions Critical for Osteocyte Survival 8 samples shares interactions, control
- GSE268719 Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation 169 samples shares interactions, epistatic
- GSE268717 Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [MNase-seq] 18 samples shares interactions, epistatic
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.