Transcriptome profiling based on the presence of Usf2 and nutrient starvation
RNA-seq (gene expression) · mouse · 16 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
- 16 samples: 8 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.
- Paper
- USF2 and TFEB compete in regulating lysosomal and autophagy genesNature communications · 2024
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 GSE252311_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 PRJNA1059624 and SRA study SRP480811. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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.
- GSM7999297 Usf2 WT MEF, Normal media, rep1 Usf2 WT MEF, Normal med…
- GSM7999298 Usf2 WT MEF, Normal media, rep2 Usf2 WT MEF, Normal med…
- GSM7999299 Usf2 WT MEF, Amino acid starvation media, rep1 Usf2 WT MEF, Amino acid…
- GSM7999300 Usf2 WT MEF, Amino acid starvation media, rep2 Usf2 WT MEF, Amino acid…
- GSM7999301 Usf2 KO MEF, Normal media, rep1 Usf2 KO MEF, Normal med…
- GSM7999302 Usf2 KO MEF, Normal media, rep2 Usf2 KO MEF, Normal med…
- GSM7999303 Usf2 KO MEF, Amino acid starvation media, rep1 Usf2 KO MEF, Amino acid…
- GSM7999304 Usf2 KO MEF, Amino acid starvation media, rep2 Usf2 KO MEF, Amino acid…
- GSM7999305 WT MEF, Normal media, rep1 WT MEF, Normal media,
- GSM7999306 WT MEF, Normal media, rep2 WT MEF, Normal media,
- GSM7999307 WT MEF, Glucose starvation media, rep1 WT MEF, Glucose starvat…
- GSM7999308 WT MEF, Glucose starvation media, rep2 WT MEF, Glucose starvat…
- GSM7999309 Usf2-/- MEF, Normal media, rep1 Usf2-/- MEF, Normal med…
- GSM7999310 Usf2-/- MEF, Normal media, rep2 Usf2-/- MEF, Normal med…
- GSM7999311 Usf2-/- MEF, Glucose starvation media, rep1 Usf2-/- MEF, Glucose st…
- GSM7999312 Usf2-/- MEF, Glucose starvation media, rep2 Usf2-/- MEF, Glucose st…
- GSE252310 Genome binding/occupancy profiling of USF2 under glucose starvation and changes in H3K27ac based on the presence of USF2 12 samples shares usf2, starvation, presence
- GSE252309 chromatin accessibility profiling by ATAC-seq based on the presence of Usf2 4 samples shares usf2, presence
- GSE248964 Isoform Usage as a Distinct Regulatory Layer Driving Nutrient-Responsive Metabolic Adaptation (RNA-seq) 117 samples shares nutrient
- GSE253945 Tissue RNAsSeq of germ-free IL10KO versus WT mice in the presence or absence of human gut microbes 108 samples shares presence
- GSE289833 Whole Transcriptome Analysis of Hypothalamus in Mice during Short-Term Starvation 12 samples shares starvation
- GSE270654 Multi-omics analyses and machine learning prediction of oviductal responses in the presence of gametes and embryos 62 samples shares presence
- GSE266466 Comparison of Ribosomal RNA profiles in mouse skeletal muscle in the presence and absence of the RNA binding portein HuR 56 samples shares presence
- GSE266586 RNA-seq in murine LSKs after Cux1 and/or Ezh2 loss, in the presence or absence of the DNA damaging agent N-ethyl-N-nitrosourea 39 samples shares presence
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.