X-chromosome upregulation operates on a gene-by-gene basis at RNA and protein levels
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 35 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
- 35 samples: 13 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
- X-chromosome upregulation operates on a gene-by-gene basis at RNA and protein levelsNature communications · 2025
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 GSE282792_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 PRJNA1190420 and SRA study SRP547554. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 26 samples.
How we read this: 13 replicated groups read from 35 sample titles; they account for 26 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.
- GSM8650584 XX Wildtype.1 XX Wildtype
- GSM8650585 XX Wildtype.2 XX Wildtype
- GSM8650586 XX Rnf12.1 XX Rnf12
- GSM8650587 XX Rnf12.2 XX Rnf12
- GSM8650588 XO XCastO129.1 XO XCastO129
- GSM8650589 XO XCastO129.2 XO XCastO129
- GSM8650590 XO X129OCast.1 XO X129OCast
- GSM8650591 XO X129OCast.2 XO X129OCast
- GSM8650592 Deletion A
- GSM8650593 Deletion B
- GSM8650594 Deletion AB
- GSM8650595 Deletion C.1 Deletion C
- GSM8650596 Deletion C.2 Deletion C
- GSM8650597 Deletion C-G
- GSM8650598 Deletion D.1 Deletion D
- GSM8650599 Deletion D.2 Deletion D
- GSM8650600 Deletion E.1 Deletion E
- GSM8650601 Deletion E.2 Deletion E
- GSM8650602 Deletion F.1 Deletion F
- GSM8650603 Deletion F.2 Deletion F
- GSM8650604 Deletion H.1 Deletion H
- GSM8650605 Deletion H.2 Deletion H
- GSM8650606 Deletion I.1 Deletion I
- GSM8650607 Deletion I.2 Deletion I
- GSM8650608 Deletion I-TEL.1 Deletion I-TEL
- GSM8650609 Deletion I-TEL.2 Deletion I-TEL
- GSM8650610 Deletion J.1 Deletion J
- GSM8650611 Deletion J.2 Deletion J
- GSM8650612 Deletion K.1 Deletion K
- GSM8650613 Deletion K.2 Deletion K
- GSM8650614 H4K16ac XX
- GSM8650615 Input XX
- GSM8650616 H4K16ac XO
- GSM8650617 Input XO
- GSM8650657 XX, XO, XY, Del1, Del2, Del3 [scRNA-seq]
- GSE282784 X-chromosome upregulation operates on a gene-by-gene basis at RNA and protein levels [RNA-seq] 30 samples shares x-chromosome, upregulation, gene-by-gene, operates, protein, levels, basis
- GSE282785 X-chromosome upregulation operates on a gene-by-gene basis at RNA and protein levels [ChIP-seq] 4 samples shares x-chromosome, upregulation, gene-by-gene, operates, protein, levels, basis
- GSE250593 mTORC1 cooperates with tRNA wobble modification to sustain the protein synthesis machinery 46 samples shares operates, protein
- GSE297249 Unfolded protein response signaling promotes myeloid cell production and cooperates with oncogenic mutation 16 samples shares operates, protein
- GSE237392 Loss of Kmt2c or Kmt2d drives brain metastasis via KDM6A-dependent upregulation of MMP3 81 samples shares upregulation
- GSE207943 Epigenetic plasticity cooperates with emergent cell-cell interactions to drive neoplastic tissue remodeling in the pancreas 59 samples shares operates
- GSE245607 WWOX promotes osteosarcoma development via upregulation of Myc 39 samples shares upregulation
- GSE231933 The chromatin remodeling factor Arid1a cooperates with Jun/Fos to promote osteoclastogenesis by epigenetically upregulating Siglec15 expression 37 samples shares operates
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.