Genome binding/occupancy profiling of USF2 under glucose starvation and changes in H3K27ac based on the presence of USF2
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 12 samples: 2 × USF2 ChIP-seq, Normal, vs 2 × USF2 ChIP-seq, Glucose starvation, vs 2 × Input, Normal, vs 2 × Input, Glucose starvation,Groups 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 GSE252310_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1059622 and SRA study SRP480812. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 8 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.
- GSM7999285 Usf2 WT MEF, Input
- GSM7999286 Usf2 KO MEF, Input
- GSM7999287 Usf2 WT MEF, H3K27Ac ChIP-seq
- GSM7999288 Usf2 KO MEF, H3K27Ac ChIP-seq
- GSM7999289 USF2 ChIP-seq, Normal, rep1 USF2 ChIP-seq, Normal,
- GSM7999290 USF2 ChIP-seq, Normal, rep2 USF2 ChIP-seq, Normal,
- GSM7999291 USF2 ChIP-seq, Glucose starvation, rep1 USF2 ChIP-seq, Glucose …
- GSM7999292 USF2 ChIP-seq, Glucose starvation, rep2 USF2 ChIP-seq, Glucose …
- GSM7999293 Input, Normal, rep1 Input, Normal,
- GSM7999294 Input, Normal, rep2 Input, Normal,
- GSM7999295 Input, Glucose starvation, rep1 Input, Glucose starvati…
- GSM7999296 Input, Glucose starvation, rep2 Input, Glucose starvati…
- GSE252311 Transcriptome profiling based on the presence of Usf2 and nutrient starvation 16 samples shares usf2, starvation, presence
- GSE190102 Ageing-Related Changes to H3K4me3, H3K27ac and H3K27me3 in Purified Mouse Neurons 43 samples shares h3k27ac, changes
- GSE252398 Genome wide map of Runx3, Brn3a, Islet1 binding, chromatin accessibility (ATAC) and Histone H3 acetylated on lysine 27 (H3K27Ac) during early development of DRG TrkC neurons 26 samples shares h3k27ac, binding
- GSE217824 Analysis of Nr1h2 and H3K27ac genomic binding targets in ESC and EPSC under Nr1h2 activation 16 samples shares h3k27ac, binding
- GSE253172 Genome wide map of Runx3, Brn3a binding and Histone H3 acetylated on lysine 27 (H3K27Ac) during early development of DRG TrkC neurons 11 samples shares h3k27ac, binding
- GSE252309 chromatin accessibility profiling by ATAC-seq based on the presence of Usf2 4 samples shares usf2, presence
- GSE232398 NKAPL binding sites in mouse testis and the genome-wide occupancy of the SOX30/HDAC3 protein complex and RNA Pol II in the absence of NKAPL 20 samples shares occupancy, binding
- GSE299628 Genome binding/occupancy profiling of transferred WT or Mek1/2-tKO CD45.2+OT-II T cells. 6 samples shares occupancy, binding
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.